What to do with income from SaaS

I own a SaaS app with a subscription model. When I (hopefully) eventually switch from PayPal to a merchant account, where should I keep the income from subscriptions? Some people have told me to put it in its own account, others to just lump it into the business's checking account. What are the pros/cons of this?

I tend to keep a couple different accounts at the bank. I keep one for operating (where most of my money is kept) and one for our merchant account (incoming) and one for payroll (outgoing). My bank can schedule things if accounts get to certain amounts and schedule things on certain days. So I have payroll scheduled to move $X from operating to payroll every 2 weeks. And I move my merchant over every couple of weeks.

No real reason to do this. I like that my Payroll company can only pull out a certain amount versus all of my operating. Makes it easier to see the transactions. I like the convenience of looking at my merchant checking and seeing those transactions versus where all our checks and other things go.

So, it's really a convenience thing, and could be a little bit of a safe guard. I don't give out my operating routing / accounting numbers. Actually, it's a money market account so I get higher interest on it too.

Doesn't cost you anything to open more accounts, at least at my bank.