You might try to find some additional reading. It's hard to get grammatical concepts fixed in the mind if you don't see it in context. 38 Latin Stories is good (if you don't already have it) and follows Wheelock's pretty closely. Cambridge Latin is more of a reading based curriculum, which might be useful as a supplement. It doesn't follow the introduction of grammar in the same order as Wheelock's, but it's still helpful. (Actually, there are plenty of teachers who swear by Cambridge Latin as the sole text, although you might want to supplement it with a little more grammar.)
The colleges around us are no longer using Wheelock. They've switched to Latin for a New Millennium and Ecce Romani. I haven't seen these books myself, but there must be some reason for the switch. Personally, I find Wheelock to be a better reference than an actual teaching method. It may work fine if you have reading supplementation and a good teacher, but on its own, particularly in the later chapters, it doesn't even bother to explain things. And one can't get the information through inference because there are too few sample sentences and many of them can be translated in a variety of conflicting ways. There are a lot of people who swear by Wheelock, but they often learned Latin in a classroom setting with a teacher who knew the language.
As with learning all languages on my own, though, I don't think there's any one method/book that does it all. I've had to cobble things together, so that when one resource doesn't bother to explain something, I can go look it up somewhere else.