hey there thematrix, you'll want to go with the Yakima Q Towers roof rack system for your 2006 Toyota Matrix. The Yakima Q Tower system includes four Q Towers, a pair of Q83 Clips for the front of the roof and a pair of Q116 Clips for the rear of the roof (this Q Clip combination is specific to your Toyota Matrix) and two cross bars. You will attach the kayak carriers directly to the Q Tower front and rear cross bars. The 48 inch crossbars are the recommended length for your car top.
The issue of cost when adding gear carriers to a base rack system is becoming more and more common as the car rack manufacturers keep ratcheting up the price of just the multi-purpose base rack system. Many people don't have much money left to spend on the gear carriers themsleves. There are soom really good cheap kayak racks luckily. My current couple of favorites are these:
1) The
Malone AutoLoader Xv j-kayak rack uses a j-cradle design for easy loading/unloading of your kayak and attaches directly to the Yakima Q Tower cross bars. This is a very affordable solution that works just as well as the more expensive models. The Malone AutoLoader Xv kayak carriers use up very little crossbar space compared to other kayak racks and will allow you to attach two of them to the 48" cross bars to carry 2 kayaks at the same time if you ever require this option.
2) The
Malone SeaWing Xv kayak rack is another excellent option that transports the kayak in the more traditional style laying flat. The unique feature of the malone SeaWing Xv however is that it has a center point attachment. Meaning you can mount this close to the edge of the base rack cross bars, allowing you the option to attach other gear carriers or another SeaWing Xv kayak rack if you want to ever carry 2 kayaks, without having to get longer cross bars (some very wide kayaks will require that you go with the longer 58" cross bars if you plan to carry 2 kayaks).