I don't even know how to answer the OP. We have more than enough coming in to cover everything. So we buy what we want, when we want, evaluating each purchase and each dollar as we consider parting with it.
We have set up automatic deductions for the IRAs, and before we even get the paycheck some money leaves to go play in a retirement fund.
Right now, we are working on paying down a HELOC (super low rate, but adjustable so we want to be rid of it). Every couple weeks, I look at the account, scoop up what is obviously extra, leaving plenty of slush, and dump it in the HELOC. When we didn't have the HELOC, I did the same thing except I dumped it in a non-retirement investment. The way I determine what is obviously extra is that I know, within each point of our pay/spend cycle, what the usual swing is. So if, for example, I am looking and it is about 5 days after the 1st of the month paycheck, I know that's the very lowest point in our cycle. So if the balance is $7000, I am going to take about $6000 out. The remaining $1000 buys me the peace of mind to know that everything will be fine even if a CC pay off (set automatically) is slightly higher than usual, or whatever. If either of us have really large expenses, I keep track of that so that I can leave more as necessary. And since I'll be looking again in a couple weeks, I'm not losing much by having that $1000 in padding. I wouldn't be comfortable not having fast access to that kind of cash anyway, so even if I carefully balanced everything to the penny, it would only be earning me about 2.4%, which is the rough difference between our HELOC rate and our checking interest rate.
So cash flow isn't really managed, other than knowing what the account "should" look like at various points in the cycle, and then just withdrawing the extra so I can put it to work.
As for paying off a mortgage early, since the topic has moved on, it's kind of no longer an option for me (mortgage is now through Bank of Parents, and part of the agreement was a standard payment so they wouldn't have to constantly recalculate, though an occasional lump sum would be find). But when we had a regular mortgage, I did pay a small bit extra. Our rate was 5.125%, but of course historically I'd do better in the market. But I considered it a bit of diversification. Just as I could expect better returns on stocks and bonds, but I still put a bit in bonds, I also put $50/mo toward the mortgage. It was a very conservative investment, essentially. And one that I put a very small amount of my "portfolio" into, at $50/mo.