The only problem that could arise from you adding your own content is if you use the exact same unique ids for your content that gets added to the official data files. Then there would be a conflict. So as long as you use unique ids that have a different form than the official ids, you'll be completely safe. For example, the ids for all merits start with a lowercase "m" prefix and merit levels start with "mx". If you used something different, you should be fine.
Assuming that the ids are different, the worst that would happen is that there would be two separate merits with the same name in the selection list. One would be your content and the other would be the one added to the core WoD data files. At that point, you could either tweak the name of your merit slightly to distinguish it or just leave it be. The two would co-exist fine.
Let me know if this isn't clear and I'll try to explain it better.
Okay... so I finally got around to trying to add some things and for the life of me can't. I feel I must be missing something REALLY simple... So I click on tools and go to launch editor. the start up screen comes up fine but when I I go to "open Data files" there are NO files anywhere in any of the hero lab files. What the heck am I missing?