Leaks... ugh! Glad you caught it right away.
So yeah, if your rig is anything like mine, you'll be able to see the red/black solar wire coming out of a little hole in the overhead carpeting in the overcab. Of course it's not as easy to see when you have the front of that whole "entertainment center" installed (I mean, come on, having your whole interior in place is so "last year"

). I'm going to take a look at mine now...
Okay, yes, at least on mine there is a hole in the carpeting on the overcab overhead kind of just behind (well ahead of) where the controller was mounted there. On my rig, this hole contains three things:
1) The black/red pair for the solar panel
2) The "phone cable" that went to the Air-con unit
3) A smallish brown wire (like say 12 gauge or so) that also went to the air-con unit.
I have pulled a couple of different wires that run through "ant galleries" in between the two roof layers, and on my rig they did come with steady pressure, and nothing broke. I pulled that phone cable as previously mentioned, and I also pulled the AC wire that fed the roof air-conditioner. The last foot or so of it (in the AC hole) was in the way of my new skylight, so what I did was pull it back (it enters the roof behind the microwave hole) so that it's juuuuust at the air-con hole and can be retrieved there, but is no longer in my way. Same thing, steady pressure and there was nothing actually clamping it in place.
My guess is that they just ran these wires through ant galleries in the Nidacore (roof coring) that is between the inner and outer fiberglass layers (outer being the actual roof; inner being what the carpet is glued to), without any specific fastening. No guarantee of course, but since you *could* run a wire in the overhead cabinets - and since it's not big enough wire for future solar anyway, it won't be tragic if the wire is broken or something (okay, by my definition of tragic, because hey, now bigger wire!).
It'll be great if you get your panel working again. It's small sure, but it's a decent battery maintainer. And it's always so unsatisfying to have various things not working.
PS: My vote would be no silicone, ever. It's dastardly stuff. Reason is, it doesn't work all that well. That alone wouldn't be so bad, but it also leaves a residue that is nearly impossible to remove, and that keeps anything (even more silicone) from sticking. I'd recommend a high quality butyl tape, but there are other good choices as well (just not silicone, I beg

) If you'd like I can send you a strip of the good butyl tape so you don't have to buy a whole roll. Most butyl tape sold now is but a shadow of the former good stuff (and doesn't work very well), but there is a boating fellow who has contracted with someone to make the "good old" stuff to specs. I can vouch for it. If you do want to buy some, it's available here:
http://www.pbase.com/mainecruising/butyl_tape
I like it because it works extremely well, and stays working for literally decades. Yet (and this is key), it is easily removable if you need to repair or redo something. Instead of suffering with blowtorches and jackhammers trying to get something like silicone OFF, you simply wipe it off with mineral spirits. (This does mean it's not good for using around fuel fills and the like). It's not technically an adhesive though, so should have some mechanical fastening too. For an adhesive caulk, I'd go for 3M4000, or a polyurethane (3M 4200). But 99% of the time I use butyl tape. It also has a long shelf life, which is a nice side bonus.