I'd be happy to share my notes, but I don't use a computer when I GM and I'm not really interested in buying a scanner at the moment.

It sounds like you're mostly worried about statting encounters. Do them by the book, at least when you first start out. 3.5's CR system varies from wonky to broken, depending on who you ask but it's a good starting point and it will mostly work at low levels.

Make a few encounters at the standard CR. It's okay if there are a variable amount of enemies. Keep 2 or 3 guys back to use as reinforcements. If the battle is hard, don't bother with the reinforcements. If it's easy, deploy them.

For the first couple levels you can probably play at CR. If the game ever gets too easy, increase the CR of the monsters you use. Up until level 6 (aka when melee characters get an extra attack) I usually use a CR of +0 or +1. Past that I go to +2. Bosses are +2 above the standard. I can't generalize past level 10 because my parties vary a lot at that point. Some are still content fighting creatures near their CR. Some optimize more and go as high as +6.

Bottom line is that you should react to how your players are handling fights. If you decide that there's a CR 12 purple worm that they're going to fight 8 months down the line, you're doing it wrong.