I don't think you're manipulating by using the money. You are right to be saving in case you have to pay for a L's retainer, which will at least be $3500. The separate account? I think you should be honest and open about it. She should know you have it but she should also know it's YOUR account.
The joint credit card has to go, but if you want to wait to see if she really files, then you can wait till then. If she files, though, close the credit card immediately.
Tough stuff. Sending you prayers for wisdom and peace ((((()))))