Hey there! I'm in a similar situation with my BF. We split our bills pro rata according to our income, but keep separate accounts. The way we manage this is as follows:
1. We figured out all of our fixed expenses that we both share (rent, internet, electricity). It's a bit complicated because we live in his condo, so the "rent" is actually his mortgage + condo fees - the principal on his mortgage (I don't have a share in the condo, so I'm not paying his principal). For simplicity's sake, if you guys rent, just use that amount.
2. We figured out your pro rata rate (percentage of the household combined income that each of us make).
3. We opened a joint checking account, as well as a joint credit card. All expenses that we jointly share (groceries, gas, rent, whatever) come out of that account.
4. We deposit on a regular basis, the amount we need for the fixed expenses, plus a surplus amount for non-fixed expenses (such as groceries or other), into the joint account according to the pro rata rate.
5. If, for some reason, one month we don't have enough to cover, we just redeposit into the account, again, according to the pro-rated rate.
6. At this point, we're pretty good at knowing how much we need every month, so we rarely, if ever, make extra deposits. After a few months, you'll be good at knowing what you spend on average. One month will be less, one will be more, but the lean months, the surplus will still be there for the more expensive months.
We have a credit card that has decent points, since we use the joint card for pretty much everything (we aren't spenders, so our only expenses are necessary living ones, hence, joint card). If our salaries change, we simply readjust the pro-rated rate as needed.
As for the expenses tracking, Quicken, Mint, or just Excel for a few months should give you a good idea of how much you'll need in your joint account generally. Hope this helps!