The fees are minimal really....
1. Using Neteller, most books offer at least one free withdrawl per month so you can cycle thru your higher balances and choose one where you still get a freebie that month.
2. A book like Pinnacle will allow an $8,000 withdrawl at no cost, so you can send smaller increments to a couple books you've lost at recently and still leave a reserve in Neteller for the next reup requirement.
3.If need be, you can always grab a small re-up bonus somewhere to more than pay for them. Even if you incur $100 in fees, its easy to offset that with a $1000 deposit to a 10% reup shop.
As for your second question...
Sure, all the time. Every night I know how I've done on the night overall but its not uncommon when tallying things up later to find yourself winning big at one shop and/or losing big at another...every day.