A Few things:
1) I am preparing to load an update to WW today. As such, I'd wait until that update is loaded before updating WW as it adds a lot of functionality for reusing props from your game and adds better decal and SubRect decal support. Watch for news of that release later today.
2) Before updating, I suggest that you copy your current WW installation to a temporary folder in case there is some essential function in your workflow that may have been broken. This is just generally a precaution/safety net. To see your current version, use the same info on line below.
3) Generally speaking, you can simply overwrite your current installation. Just make sure that you install it into the same path as it already was. You can find this path by running WWMT once and then hitting F11 and typing: wallworm_installation_path + ENTER.
4) When loading updates to WW, I recommend that you test temporarily on COPIES of your files just to make sure that the system is working as you expect. This gives you a chance to see any differences--and if there happens to be a bug, you can report it and I can fix it--and you still have access to the original files.
5) The issue of non-square textures is fixed in the VMF/Map importer from Source to Max. I think it is in the current VMF exporter, but honestly I would need to test to verify.
6) In my opinion, you should update. But please take all the notes in consideration above. Of course, if you have any issues, just post here and we'll figure them out.