AE CS6 Camera Tracker with Optical Flares

1) complete your track with AE's 3D Camera Tracker
2) select a solve point(s) and create a camera & a null
3) create a light
4) Shift+Parent (new technique in CS6) the light layer to the null
5) create a solid for VC OF and set it to use the light

Ah, just realized that you didn't specify the type of lens flare. If it's a 2D-only Lens Flare, the follow steps 1 & 2 above, then
3) create a black solid and apply your lens flare
4) apply the following expression to the flare's generating point -
//
TargetLayer = thisComp.layer("Track Null 1");
TargetLayer.toComp([0,0,0])
//

5) set blending mode of the flare solid to screen or add

HTH
RoRK

Intensive AE & Mocha Training in Singapore and Malaysia
Adobe ACE/ACI (version 7) & Imagineer Systems Inc Approved Mocha Trainer

If you're using Video Copilot's Optical Flares effect then just follow the steps I've provided.VC's OF has a Positioning Mode property that allows you to apply a flare to an AE Light.

The tutorials from VC for OF are really good. You should spend time on those if you want to get the best out of the effect.

HTH
RoRK

Intensive AE & Mocha Training in Singapore and Malaysia
Adobe ACE/ACI (version 7) & Imagineer Systems Inc Approved Mocha Trainer