APP is Automatic payment program.
Automatic payment program (APP) is use to clear and post open items. The entries related to tax, discount, and interest also get post automatically. Automatic payment program reduces manual work load of end users. Automatic payment program is a time saving tool for end users. TCode F110 use to run automatic payment .
The Automatic Payment Program does not check the Balance of your Bank Account.(GL A/c. Bal.)
What it does check is the min & max amounts that you have maintained in your customisation.
In FBZP Transaction (type in easy access screen), you have to maintain the config for your automatic payment runs.
In Bank determination (in FBZP), you have to fill in the available amounts for each Bank. This is the maximum amount up to which payments will be generated by the Auto. Pay. Run.
So if you want to ensure that on any single day the payment run does not pay more than bank balance, you have to update on a daily basis available balance to match with your bank balance .
In SPRO you can find the customisation for A P Run, but FBZP is the old transaction for the same thing. Plus it lets you do all the related customisation, in one place.
As far as I know, there is no direct way of linking your GL account balance to the A P Run.
Related: PFCG Roles and Authorization Concept