Can't you just maintain USD balances at both, and execute the trades simultaneously? Don't they have free methods of withdrawal (that take a few days). If you have a buffer of BTC and USD at both you should be able to execute your arbitrage and even the balances out periodically right? Am I missing something?
Yes, that's what I suggest too since funds transfers may take much time.
But you can't deposit to btc-e or withdraw from btc-e without fees (unless you use btc-e redeemable code). If you live in the USA, you can withdraw almost for free with Dwolla, but I am not sure what is the best way to deposit to btc-e from Dwolla. OKPay is probably the easiest option and not that expensive. It also offers a debit card, so you can cash out with ATM
