I had a 2 liter bladder that I filled all the way up for the first 5 days or so. Then I got smart and saved a half liter Aquarius bottle that fit nicely into my side bag.
I became VERY dehydrated my first day. We're talking orange urine, probably should have seen a doctor dehydrated. After that, I made water my top priority each day and never had a problem again.
My water routine went like this:
1. In the morning, check the guidebook to see what the water situation would be like. Lots of fountains and towns? I'd fill the water bladder halfway. If it was a desolate stretch, I'd go 3/4 or all the way full.
2. Fill up my half liter bottle and drink it. And repeat. I started each day with at least a liter of water in my system, whether I was thirsty or not. Some mornings I had to force it all down, but it was worth it.
3. Refill the half liter bottle and head out. I drank out of the bottle, keeping the water in the bladder as a reserve.
4. Refill the bottle at almost every fountain. If I came to a fountain, the first thing I'd do is look for an agua non-potable sign. If I found one, it meant no refills there. If there was no sign or an agua potable sign, I figured it was safe to drink. A few fountains seemed a bit suspect, and I skipped them. You'll have to use your own judgment. The next thing I would do is make sure the @#!*% thing actually works! If the water flowed, it was clear, and had no funky smells, I'd refill my bottle, drink it, and refill again. Obviously you don't need to do this at EVERY single fountain along the way. But I liked to change out the water in my bottle whenever possible, just because cool water is a little easier to drink than lukewarm or hot water.
Following this system, I only found myself without water 1 more time along the way. But that was near the end of the day I walked for 24 hours straight and I don't think my brain was working quite right!
For my second pair of shoes, I picked up a pair of these:
http://www.walmart.com/ip/AVIA-MENS-QUICKSTER-SNEAKER/33878278
They were cheap, lighter than Crocs or sandals, and they spaired me the indignity of having to wear flip flops.