BUT, (1) after-tax contributions and associated earnings can (theoretically) be isolated from (2) pre-tax contributions and associated earnings, thereby presenting opportunity to be more surgical & strategic with 401k & "QRP" conversions.   

We are wondering how people with with our situation handle where money from two contributing parties that is used for buying rentals and flips is kept.

It’s important to be objective with your prospective tenet evaluations, but I unfortunately have been the victim of a situation where a cat contributed to around $1.5K in damage because of irresponsible pet owners (key point).

You could just take the returns and split them per the equity structure though, based on each person's capital contribution - pretty straightforward.

If you bump up your rent to offset the amount you WONT get from the tenant the missing contribution from them should be moot. 

It seems like most people are wanting to go the other way to make leveraging simpler and contribution limits higher.

So if half the income goes to a partner personally and the other half to a S-Corp partner, then no diff - I AM NOT A CPA OR TAX PROFESSIONAL ASK ONE BEFORE YOU DECIDE ANYTHING.Reason I like S-Corps is you can bump the benefits (eg retirement contributions) as long as all employees are treated equally. 

I'd also say use it to juice up your retirement and medical (HSA) pre W2 contributions which is what wife/myself do. 

My monthly expenses are $4500, my monthly income is $5000 after taxes/contributions, my wife’s income is $4500 after taxes/contributions.

There are other more important factors that contribute to building a good credit.Debt/income, credit use, credit history, payment history, credit age, etc.