If you're modifying the forums feature to customize it you should clone it, and only modify your custom copy and it should use its own tables not the same tables as the included feature.
Going forward with a clone you would have to manually copy and paste changes I make to the official forums feature if you want to, but if you just modify it directly then you are making it difficult for yourself to upgrade without losing your customizations. The whole idea is to keep all your custom code in your own projects and then it is much easier to pull the latest mojo code and merge it. Once you make changes to mojo code then you are stuck maintaining your modified version and have a more difficult task to merge the rest of mojoportal and you can never use official release packages but always have to make your own custom build.
If you go down that path of making changes directly to mojo code it is scary to get the latest changes, if you stay on the recommended path and keep your custom code separate it is easy and nothing to be afraid of.
Hope it helps,
Joe