Two ways to get HIDs into your vehicle, either through a conversion/rebased kit (XenonDepot, etc) or retrofit.
A conversion/rebased kit is sticking a HID burner into a halogen setup. The seller of those kits usually moulds or through other methods attaches a halogen base, H11 for a 2006+ 4Runner, so the HID burner will fit right into the halogen housing. This is the cheapest way to get HIDs in your vehicle. However, this is also the worst way to do it. Why... the optics (reflectors, projectors, lens, etc.) in a halogen setup is engineered to maximize the dimmer output. There is always glare in a halogen setup, part of the reason the glare is to help light up overhead signs. By putting in HIDs there is now three times the amount of light and glare. Halogen reflectors are typically horrible for HIDs and there is a lot of glare. Halogen projectors are better, but it still doesn't make it ok, because there is glare and in the 4Runner's setup the squirrel finders create the glare. Member lawwailok has a detailed thread about getting rid of the squirrel finders.
As madpuma13 mentioned, a retrofit means all of the halogen components are gutted out and HID components are swapped in. Most people who do retrofits will prefer to go with HID projectors because of the sharp cut off and size of the projectors makes it easier to get everything inside and building a shroud to cover up the HID projector. It is possible to use HID reflectors in a retrofit, but because there are limited number of cars that come with HID reflectors and hard to find a HID reflector that will match up closely to the headlights of the non-HID equipped vehicle, it's just more difficult to accomplish and better results are available with HID projectors, so why bother.