First you need to figure out if you're going factory or after market.
The factory bars might be easier to install but some times they have MUCH lower weight ratings. I know in my case it was almost half of the after market systems.
2nd there are two major brands, Thule and Yakima. They both offer round, square, and oval bars, and they both have a ton of kayak mounting offerings. Because these systems are slightly universal you have to put them together to specifically fit your car.
Example you might need a footing adapter (Yakima calls them a "landing pad") to attach to the pre installed track or to anchor points. 2nd you will need the tower (Q Tower/Control Tower) and then lastly you need your cross bars. These come in several lengths and I'd go as wide as you can in the event you need to haul 2 boats.
As for the kayak holder or saddle, there are options out there for play boats, stacking boats on their side, and for wide flatter bottomed boats.
Personally I'm 100% Yakima, and use the "Even Keel" saddle system, its under $100 and comes with the straps to tie the boat down.
I'd suggest heading on over to
www.etrailer.com (don't work for them, just think they are great people with FAST service) and plug in your make/year and see what they have to offer. They are out side of St. Louis MO and their shipping department is FAST, also they beat everyone else by $40 on the full install setup that I went with.
Hope this helps!
PS: Install was on an 08 Honda Element. Factory bar weight: 75lbs, Yakima... 160lbs.