I also have no software for monitoring.
I look at three reports each morning (kite suspect report, large transaction report, large overdraft report). Being a small institution, I recognize a lot of the customers on the lists and can explain the various activity... but if anything looks out of the ordinary, I look at the items making up deposits and where checks are being written.
I also review a list of customers that we code as "high risk" and do the same kind of manual monitoring that you mentioned above.
There are all sorts of reports you can probably run, but if you don't have software to recognize unusual activity, it seems like what you're doing manually is the only way to go.
But if someone else monitors manually & does something different, I'd like to know as well.