I have a rack (Yakima) on my van to carry two Cobra Fish-n-Dives (36" beam S.O.T., very stable but S-L-O-W. I'm building a Ches. LT18 for touring) I have rollers on the back & cradles on the front. Reasonably secure & convenient (the rear bar w/rollers is right by the back of the van since I have full-length rain gutters). Heave the bow up onto the roller, then scoot the boat into place.

Stackers were not a good option for me-- 3-foot wide boats sticking up above a mini van made for a package taller than I wanted to deal with (and I'm 6'4"!)

Three suggestions:
1. if you go with a commercial rack, I think the Thule racks are better than the Yakima. The round bars of the Yakima tend to rotate in the towers, and the cradles rotate on the bars. I don't think the frustration is worth the small price saving, but YMMV. I can't comment on other brand racks.

2. Get extra-long bars and mount half of the cradles outboard of the tower (or across where the tower connects). You can carry boats wider than your roof. This is most practical if you will be removing the rack when not carrying kayaks - you won't have these bars sticking way out past your roofline to bonk your head on!

3. There are some cradles that boast a surface that lets the boat slide easily. This may be a better choice than the rollers, which can clog with sand. (I don't have experience with those cradles, so I can't say)

After my boat's in place, I put a length of foam pipe-insulation between the roller & the hull to provide a better fit of the hull contour and spread the force over a larger area to reduce the chance of denting. Don't know if this would work for you, but it's cheap enough to try.

A bow & stern line are a good idea in addition to whatever cross straps you use. If nothing else, you can see them while driving & if they start dancing around, you know you ought to pull over & check your load. Plus they're good insurance in case of strap, cradle, or rack failure. (One club member tells the tale of seeing his entire rack, with boat attached, go bouncing along the freeway - ouch!)

Have fun!