I want to try to finish answering the questions you asked. They may not be in the order you said, but I want to try to stay on the topic without getting too far away.
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We have to let them do what ever they want to do while still m.
You have already read how we cannot control what the S does or doesn't do, right? However, what you decide you can live with....or can't live without, is entirely up to you. You have control over your life and you make decisions about the matters that affect you. If your S violates your relationship boundary, or goes outside your religious beliefs/bounds, breaks the wedding vows, does something that is having detrimental affects on your children/family, breaks the law (and there are probably some other areas I won't take time to mention, but you get the point)....then you should approach the S early on when it first begins. That is the time to have the calm talk to express to the S how those actions are affecting you/family/M/etc. If your S chooses to continue her actions instead of respecting your request & feelings, then you confront her with your boundary and tell her what you will do if she chooses to continue with her actions. No threats, no pointing fingers, condemnation, etc......you just tell her what "you" have to do if she continues. If she still doesn't end her actions, then you enforce your boundary by doing whatever you said you would.
You see, we can't throw this boundary stuff around just b/c we don't like some small behavior (but for the record, there are usually other ways to handle these behaviors or bad habits). I believe it should be something serious that has bad affects on you/family/marriage and all that is precious to you. If you start flashing your "boundary badge" at every little turn she makes, it will loose its position of value.
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We can't ask questions, where they've been,
It depends. If it is related to the issues you have with her actions and if you have approached her about the issues. It depends on your plan and how you've determined to proceed. Are you giving her space and time, or are you in the LRT, or are you asking her to give account......what is the reason behind the question?
If you are dealing with a WAS/MLC, they usually take this as the LBS is drilling them and they feel like a child having to answer to the parent. Therefore, more rebellion is likely to come as a result. Usually, they react b/c they feel guilt or pressure from the LBS. If the H is asking her whereabouts just to see what she says (b/c he is suspicious of her) or is trying to control her, then she usually senses it and will begin a fight. It's the incorrect persona/image for the LBS. Unless you are ready to enforce your boundary (if it has been previously discussed), this route of questioning the WAS/MLC doesn't lead to anything positive. They see it as a control method and will react negatively.
If the LBS is giving the time/space to the WAS/MLC, he is being confident, being cool, nonchalant, staying calm, showing a positive mental attitude (without acting goofy), getting a social life, etc., that isn't about her. None of those things are directed at her, but she sees you being all those great things. It's like you give her the time and space to see you being happy with or without her.....and living with or without her. She is free to be in a MR with this wonderful man that you are showing you can be, or she can choose to leave.
At the same time the LBS is giving the WAS the freedom, he puts that time to use wisely by really putting himself through a personal boot camp. Every area....every thing about him is improved, corrected, or polished. You use the time to get informed and go to work changing the inner struggles you have.
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can't defend ourselves when in an argument,
I'm not sure about the context in which you are referring, but why are you defending yourself? The point is that if she talks at all, you role is to listen. If she's mad and digging up your faults, throwing everything in your face....it's not the time to defend yourself. It is the time to set there....looking into her eyes while she's talking, and keep you mouth closed. Even if you can't agree with what she may accuse, you can nod your head (or not)to show her you hear her. Sometimes, a woman can feel validated just if her H really hears what she's saying. You don't need to say anything except you are listening.
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we have to try not to act like the a is affecting us.
Again, I'm not exactly sure how you mean this. IMO, once you have confronted her about it, what or how can you act that will change her mind and end the A? There have been so many men who have told us how they plead, cry, beg, agree to anything she wants them to do...if she will only end the A. Some men are outraged and try to police what their W does....trying to make her end the A. Guess what? Neither one works.
I believe it is not a good thing for the W to know that YOU know about her A....and you just live with it. It is one thing to back away and give her some time & space to get her act together, but it's quite another for her to flaunt the A and continue to live with you and the children in your home. It is about the most disrespectful thing a W can do. If she continues the A without any consequences to her MR, then she will detest her H and really wipe her feet on him.
There is a lot to be said on this topic, but I hope you get the point.
As for the part of going "dark", I do not advise this step for your plan. It is almost impossible (but not entirely) in a co-parenting situation. Going dark means exactly that....no contact ever.
I would advise you to get legal advice in order to protect yourself and your children. See where you stand in your state about your house and other property, finances, child custody/support, father's rights, etc. A lot of advice here on the board is handed down through the years. Some of it may apply or it may not. When it pertains to legal matters, don't just take our word...but check it out.
Set up a visitation schedule for when each parent has your son. Holidays are here upon us and emotions are fragile for your family. Try to be fair and agree on the times each of you will spend time with him.
Your greatest challenge will be to pull back. She will probably enjoy her new found freedom and play like she's a new single girl. The more distance you put, the better for you. As a warning....WAW's will cake eat if you serve it.
So, start with getting legal advice(have your questions ready). Put a visitation schedule in place. Enroll in your personal boot camp. Set small weekly (or daily) goals for you to accomplish. Write them out. You can use this board as a journal, if you want. But make these goals about "you" and the man you want to become. Accept the fact that she may come back home and she may not, but you are going to be fine either way. "Being fine" is up to you. You are responsible for your happiness, nobody else can do it.
What do you want your W to see when she comes to the house? Think about this for awhile.
It is not about what you feel should work in your M. It is about doing the work that gets the right results. Do what works!