At the start of each turn I always check my profits before I build anything. Then I go through each settlement and if I have the money make sure it is building something and keeping its garisson up to date. To help me remember everywhere, I tend to dividie my empire into regions. As the HRE I own most of Europe, so first of all I check through my Italian places, then Spanish, then French, German, eastern, Scandinavian, and British provinces.

After that I check the armies on each battlefront. I check taxes etc while I have the building scroll up.

The agent tap is usefull early on, but once I have a team of 15 Priests I don't really bother with it. It really should be split up for each agent type. So I do make mistakes here, everyone forgets to move a diplomat a few tiles closer to Sarkel sometimes.

As for beating enemy armies, don't draw up a spreadsheet. Use your spy to see what they've got, besiege a settlement so they have to come and attack you to relieve it, and if you have enough forces you'll just need to try and defeat the AI on the battlefield, which is a whole different game. Generally though, if the forces are equal you should win.