Shannon - don't feel guilty, the important thing is that he's doing better and gaining weight like he should, not how you feed him!
I'm rusty on breast milk storage - you might want to pop over to Breastfeeding to see what they say. You can always freeze it, and I think it's ok in the fridge for a few days.
You should pump as often as you would feed, so with a 6 month old you were probably feeding him every 4 hours or so, so you'll want to pump that much to keep up your supply. Don't worry how much you're getting - just pump what you can - again - you might want to check with the BF girls on that. Personally, when we started to wind down BF, I just pumped as much as I could and then topped DS' bottles off with formula. Some EBM is better than none!
Why are you giving him water? I've not heard of doing that unless it's very, very hot where you are?
Hang in there - and meanwhile, I'm glad your lo is feeling better!