Yes, that will be easier to do. Even opening each from the same account separately.
The -prune option is from command line start?
You can put it in the bitcoin.conf that should be in the data directory. The code is:
-prune=n
where n is in megabytes. So if you want it to be a max of 5GB, it will be -prune=5000.
Take note that you cannot import any private key nor change the wallet.dat once you enable pruning. If you do that, you will have to download the blockchain all over again.