For the Yakima fit, here's what I did when we had the '98. I couldn't find a single picture of my rig to help illustrate what I'm talking about though.

You can get by with the regular tower, but if you are mounting toward the rear you may not have much clearance between the rear cross bar and roof. That made it difficult for me to mount many of the Yakima accessories. Probably OK if you are planning to mount a cargo basket with u-bolts though.

On the '98 I took off the factory rack. I already had the Yakima 1A towers so I purchased the hi rise kit which is basically the spacers and additional hardware you get if you buy the hi rise towers as a package. I cut the hi rise spacers down so the rack didn't look so freakish and the crossbars sat closer to the roof. If you go this route you have to replace or shorten the bolts that run (vertically) through the spacer. Hope that all makes sense.

Not that I ever had a problem with the Yakima (it is still going strong on the '89), but if you are going to put a cargo rack up there and load it down, I like the Thule towers because they are one solid piece of metal vs the composite yakima tower.