Early in our sitch, we split things from one join account into three: her personal account, my personal account, and the shared one (for house payments and any other joint bills). We each have our paychecks deposited in our personal accounts, and then transfer a "fair", set amount from there to the joint account. When W started hinting around about this, I did a 180 - said "that's a great idea" and set it all up.
As far as the bonus, I would not treat it as anything "special". Instead, I would go with "My annual income is $____ (includes both salary and bonuses) and I will contribute x percent of it. Your annual income is $____ (includes both salary and bonuses) and you should contribute the same x percent of it." This is what we did (making some adjustments for who pays for health care, etc.) and we both consider it fair and reasonable.
Thread #10 22 year M, MLC, Piecing since 1/07 Goal: Live with confidence & enthusiasm!