If your doing something time sensitive, always pay through your wallet. That way if the exchange is having an issue you will not be affected.
If you are worried about your coins staking istart your client with the reservebalance command line argument, which will make the specified amount of coins ineligible for stake by the client. If you put an amount in that is larger than your total coins, it will essentially turn off POS mining and therefore staking with your coins.
An example batch file to launch a client with the argument in Windows can be seen below. Make sure you change the relevant paths to match your own.
@echo off
start f:\cachecoin\cachecoin-qt.exe -reservebalance=100000
exit
Hope this helps.
Hm, as I don't have any technical knowledge about wallets etc, I don't really get this.
I've got a new wallet now, the newest version with 0 coins. What happens when I withdraw my coins from Cryptsy? What means when they got 'stacked'? Will they got stacked when I withdraw them now?