If you have any installed games prior to installing Galaxy, these won't be picked up automatically by the client. Any recent offline setups installed after Galaxy will be recognised by the client.

If you will want to add your currently installed games (or some of them) to the Client after installation, you will have to pick Scan Folders option in Galaxy. To add only some and exclude others, check game folders first for goggame-*.info files. Removing these files should be enough for Galaxy to 'ignore' the game during scan.
( ^ that's also why some of the older installers aren't picked by the client and cannot be imported. They lack necessary .info files)

To stay on the safe side, you could install Galaxy, change its options before first login (turning off autosaves, setting default folders etc), check your existing games for .info files and adding these that you want to the Galaxy one by one.

Be mindful though, that adding a game via folder scanning *will* trigger an initial update to the latest available version, regardless of auto-update settings.

If you do decide to try out Galaxy and you encounter issues, please don't forget to visit our bugtracker:GOG Galaxy bug tracker link

You can probably do this reliably with DOS games but I wouldn't tempt fate with newer games since nowadays a game will store its saves in a wholly different place than the actual executable (hello games that store saves and such in My Documents!). That's not even getting into the registry and the like.

Both WC1&2 are DOS(Box) games and thus keeping them intact should be fairly easy.
Just drop me a PM tomorrow if you have any questions / concerns and I'll walk you through a backup or some workarounds to keep both versions functioning.

Unfortunately I don't have access to that and best I can do is to ping Galaxy team on Monday, sorry.