What I do is send all of my bitcoins I want to move to savings into a specific address that isn't even on my wallet. If I'm understanding this correctly, the wallet.dat file on the USB stick is just a backup of the one currently on your computer's bitcoin wallet, so here's what I would do:
1. Make another backup of your current wallet.dat
2. Open the bitcoin wallet, and create a new receiving address.
3. Send all the bitcoins you want to save to that address.
4. Go to help->debug->console
5. Type, dumpprivkey <address from step 2>
6. Keep that private key on your usb stick instead of the wallet.dat
7. Go to appdata/bitcoin and restore your wallet.dat from step 1.
Now you have:
A Bitcoin wallet on computer for general bitcoin transactions, and a separate address not part of your wallet to send bitcoin savings. To spend the coins from the saving address, simply go to help->debug->console and type importprivkey <private key from step 5>
But that's just me.