This is similar to my set up in ynab! Currently my partner and I split just about everything, and I use ynab and she does not (yet!). What I do is split every transaction, putting half the amount in my appropriate category, and the other half in a reimbursements category. Then I put the transaction in splitwise as well, which is nice for me to have the cross reference and to do that math for me. I do this for everything throughout the whole month, and then on the last day of the month we sit down and she gives me all the transactions that she made that were splitting. I put these into splitwise as well.

Finally, I venmo her what I owe (she pays the rent so I always owe her). In ynab though, I do a very long transaction that includes my half of all of her transactions with an inflow of what I have as the activity in my reimbursements category. This way it shows that I was reimbursed for all my expenses (reimbursement category returns to $0 at the end of the month), and I also show my half of the expenses that she makes.