Best way IMNSHO is to just "gloss over" how and just assume the Fixer got his fee. The monetary awards for the run should be going entirely to the PCs, not split up (also paid per runner and not lump sum to be divided). I as well firmly believe that an extra sum should be given for expenses like bribes and other cred spent in legwork--as well as expenses incurred like ammunition expenditure and the like. The pay should be enough to cover a middle lifestyle for either one or two months with enough left over to be able to start seriously saving for more (or upgraded) gear/implants.
Sometimes a Johnson will pay per runner, and sometime by the job. Depends on the situation. If the runners don't like the lump sum, they don't have to take the job and can go another month without getting work. A few months of not getting work becuase they think they're better than everyone else and deserve better than the next runner will bring them back down to earth.
You are right, the Fixer's fee shouldn't come out of the payment going to the runners, but the players need to remember that the Fixer is getting paid by the Johnson, and their screwups look bad on him (or her) too.
The pay should be based on the job. If it's a milk run or cake walk, they shouldn't be getting 10,000+ nuyen each for the job. I personally gauge the fee on the difficulty and the equivalent lifestyle for each runner in the group. If it is an easy run, enough for low lifestyle for a month. Moderate run should pay medium for a month. Difficult should be high for month. Freakin' Hard should be 50,000+. Of course, I'm offering up more than just one run per month, sometimes two, and if they are lucky, three.
The ammo and contact expenses, the Johnson won't, in most cases, care to cover. Too many low lifes in the shadows have taken advantage of that. I've even had runners tell the Johnson that they burned off grenades, rockets, and APDS ammo, and walk away with a whack of cash. A good story and con roll will convince the Johnson, and so they would only let this happen once or twice until they put a stop to it, and word on the street would travel to all the Johnsons, effectively altering their negotation strategies.