I own Guitar Breakthrough and did a review of it here on this site:http://www.guitarnoise.com/review.php?id=178
It's a good software for beginners. If you've read any of Len's articles here on Guitar Noise, you'll have a pretty good idea of what the style is like. For someone starting from the ground up, it will do you well. Being a CD-Rom, it's much more into visual than text and even has some simple and fun interactive pages. The only drawback I can think of is that you might find it too easy.
But I've got to caution you on something, and this is based on my own experiences with my students who are in similar situations (lots of experience, little to no theory). There's a tendency, when in this situation, to find almost everything about theory boring. Doesn't matter how artfully or entertainingly it's presented.
You might find it easier to simply take a chunk of theory at a time (and it doesn't really matter much what source you use) and then mix that up as much as possible with what you already know.
With most guitarists in your situation, it's not that they don't know theory - rather it's that they don't know what they know! What you may actually need from theory is not the theory itself but rather the ability to interpret what you know the same way other musicians do.
And you might find this best done with a teacher. You wouldn't need a lot of lessons and could probably even do something on a once a month basis or so.
These are just, of course, my thoughts on the subject. I'd be more than happy to chat with you more concerning this, either here or you can email me directly.