Is there any issues I should be aware of in doing this? "Be careful you don't do *this* or you will lose everything!" kinda thing...
Just to clarify, you are describing two completely separate wallets, right? i.e., not hoping to copy the wallet and use that for the second instance.
Yes, the one with most of my btc will be in a truecrypt directory, which I won't have to access too often.
The other will be a daily use wallet with a small amount of funds.