I really like Delfina's advice.
What's important to remember when you're in that situation, is that unless you strip every stall every day and then add new shavings, you're not going to be able to make a stall perfect in a reasonable amount of time. What I always did was remove the pee spots and all the poop I could get. What I did after depended on the barn owner- one liked new shavings added and then raked, with no shavings on the edges of the stall, one just liked new shaving added, one liked certain stalls done a certain way, etc. That way, most of the time, the stalls were pretty good until whatever time it was decided they needed to be stripped.
Some stalls get to a point where they just need to be stripped, no questions about it.
So, to get to my point, use your best judgement.
I'm not sure why people are mixing pee in their horse's bedding. You remove the pee spots first. You shouldn't be mixing clean or fresh bedding with pee.
Depending on how bad it is, you might need to strip all the stalls and start from scratch. If the stalls are really bad, you can spend all day in them removing stuff, but you're never going to really get them cleaned well. It sounds like this might be your situation:
These stalls are so dirty and there's tons of bedding.
The bedding in the stalls is brown from people mixing it around with pee.
I could spend all day in each stall looking for poop.
If you really feel the stalls should be stripped, talk to the owner of the barn. Explain things. Ask if anyone would be willing to help. Do you have any equestrian friends? Maybe they'd be willing to put in some time with you. Sometimes, you just need to get to the bottom of the matter. It may be painful, but it will be so much easier from there.