I noticed that in the 2005 manual, Chinook no longer published a diagram of the DC system. However from what I have gleaned, plus looking at the diagram they do have of the "brown box' area, I think there's a good chance it's similar to what I (and others) have. So I'll describe my original setup to you FWIW.
Starting on the roof, there was a 55 watt Siemens panel on the forward portion of the passenger side roof. It was held on with aluminum angles fore and aft screwed into the roof. Under the middle of the panel (invisible until you remove panel) was an SAE style connector with one half on the solar panel wires, and the other half screwed into the roof. Like so:
Panel half:

- connector on panel.jpg (12.97 KiB) Viewed 2440 times
Roof half:

- connector on roof.png (53.66 KiB) Viewed 2440 times
Under the flanged roof connector was a hole of about 5/8" diameter. The wire went into that and forward, between the roof and the ceiling (in other words it tunneled through) and came out in the ceiling of the overcab on the far passenger side, through a slit in the ceiling carpet. From there it went into the solar controller (such as it was...), which was in the passenger side of the "entertainment panel" by the passenger side stereo speaker (not sure where yours is).
From the solar controller, the wires (one red one black) went down into the passenger side pillar, briefly, then across to the driver's side between the headliner and the cutaway cab. Then down the driver's side pillar and out a hole in the floor (behind the pillar) and to the battery compartment. Shortly before the attachment to the house bank was a 7.5 amp inline fuse, and then the wires attached directly to the house battery terminals.
Yours may not be exactly the same, but on the other hand it may be rather similar. I don't see any solar wiring listed in the 2005 manual on the "brown box' diagram, which makes me think it runs right to the battery like on mine.
Not that you asked but I wouldn't re-use any of that wiring. It's too small for any but the smallest panel (or major voltage drop). In fact, I can't see any good reason to have the solar controller so far from the batteries. Most decent ones have a remote display, so you can put the controller close to the batteries (and even if no remote display, more important to have it function well than to have it in the OEM spot, IMO). They got away with it because it was a 55 watt panel and never intended to do anything other than keep the battery up when parked (i.e. not camping). Plus solar was a lot different (and more expensive!) then, and knowledge was less.
Here is the DC diagram from the 2000 Chinook manual. I colored the solar panel, wires, and fuse (sorry it's a bit blurry - it's an excerpt - but you can click on it to at least enlarge it). You might find the earlier manuals helpful as they did show more in the DC diagrams and etc. I believe I uploaded them to the Documents/Reference sub-forum.