I deposit whatever the minimum is for the site's deposit bonus, or $300, whichever is greater. $300 because I need that much to be comfortable playing at $1/$2 limit tables. Once I make the transition to $2/$4, that minimum will be $600, etc.
I cash out whatever I earn at a site to my NETeller account, in increments of $200. Of that, half goes into my bankroll (well, half STAYS in my bankroll, I should say) and the other half goes to my bank account.
The exception would be if I'm depositing at some site only to play in a CC event, but if I deposit to actually play, I won't go in with less than $300.
I also like to keep $600 in my NETeller account at all times for when Stars decides to do a reload bonus. Those are pretty easy to clear, and I really like PokerStars