Ahhh... that's ok

Do you have two darkcoin.conf (darkcoin1.conf and darkcoin2.conf for example) and only one wallet.dat? Is that how you want it to run? If it is I guess you can't start two masternodes that way for now (until 0.10.16.x is officially out) because when you issue "masternode start" command it will search through vins that wallet.dat contains until it finds FIRST one with 1000 DRK. Then it stops and use this vin to start masternode. So basically when you switch configs you will find the same FIRST vin again and will never proceed to second one.
To run second masternode you have to have second wallet with 1000DRK.
The best way is to create two fresh wallets and import corresponding private keys in each one to be able to start masternodes while having your original wallet just to have control over all funds you have. That's the way I did for myself actually
In short:
1. backup your original wallet.dat somewhere else just in case
2. open qt-wallet, go to help -> debug window -> console
3. enter "dumpprivkey YourDRKAddressThatHave1000DRKs" and save the output somewhere in txt (do this for every address you'd like to turn into masternode)
4. close qt-wallet
5. make sure you backed up wallet.dat once again

6. rename wallet.dat to something else (I prefer "main_wallet.dat" just to keep things clean)
7. open qt-wallet (don't forget to use correct config in -conf parameter) and let it create empty wallet (this will take a while)
7a. OMG you have 0 DRKs now! PANIC! Well, not really

8. go to help -> debug window -> console
9. enter "importprivkey OneOfTheWeirdOutputsYouGotInStep3"
10. you should see 1000 DRK in your balance right now (or may be you have to restart qt-wallet not sure about it)
11. issue "masternode start" just like you always did, close qt-wallet and ensure that masternode is running (that grep command in guide)
12. rename wallet.dat to say "masternodeN_wallet.dat" (N=1,2,3,4 and so on) and repeat steps 7-12 again for your next masternode (you can pass step 7a now

)
Once you've finished you should have main_wallet.dat, masternode1_wallet.dat, masternode2_wallet.dat and so on.
You have to make copy of one of these wallets and rename this copy to wallet.dat to do different things:
to use as usual - copy "main_wallet.dat", to start/stop masternode X - copy "masternodeX_wallet.dat" (don't forget to use correct config in -conf parameter too)
NOTE: DO NOT RENAME OR DELETE WALLET.DAT WHILE QT-WALLET IS RUNNING
That's not that hard as it might look and maybe you can even script it in some way but I'm linux/macos guy and I don't know if it's possible on windows
EDIT: fixed version number 0.16 - > 0.10.16.x to avoid confusions