Hello,
I am shooting an event this weekend with a JVC GY-HM600u and as a second camera a Canon 5D markii. Any tips on the settings on each camera to best match the shots. I will be editing in Adobe Premiere Pro CS6.

Oh boy. This might be a stretch. To make your editing easier you want to make sure that the colors are at least similar. This is very hard if you don't have a live test rig set up or some way to compare outputs live.

First set both cameras up and film a color test chart or a live subject under decent indoor lighting with the shots being visually as close to each other as possible. Same zoom, exposure etc. Compare the two in your program. Look at the vectorscope and waveform especially. Canon cameras tend to be warmer than JVC cameras so you might want to adjust the JVC that way. Keep adjusting and looking at the resulting files until you get what you like. This can take a lot of time. I would rather make a color adjustment preset in the editing program and apply those to the appropriate clips when editing than try to adjust the cameras without the appropriate live equipment.

To clarify a couple of things I wrote yesterday, by exposure I mean luminance level not f-stop. The cameras are so different that sensitivity levels are expressed in different terms. For example, 0db on the JVC might equal 200iso on the Canon. Might is the word here. You'll find out. And you might find the JVC f-stop at 2.8 and the Canon at 4 when they have equal exposure on the same subject, don't worry about that. So the point is to use the lowest sensitivity possible on each camera during your test filming to start and then later see how the camera color images change as you raise the sensitivity for low light filming.

Also by "live subject", I mean a human, not a pet. What you need to see is how each camera reacts to flesh tones.

Thanks for the advice William. Yes the color balance/match are extremely important and I did not have the time or a monitor to match the 2 cameras prior to the wedding. Also there were multiple location/lighting changes which would have made things even more difficult.
I was more curious about matching frame rates, record formats Avchd, mpeg4, QuickTime. Originally I was planning on using AVCHD as my rec format but did not have a 24p option on my JVC and I did not have a 60i or p option on the 5Dii.
Although any setting matching insight would be appreciated. This was my biggest hurdle at the time.

I am not sure how Adobe Premier Pro responds to different file formats when using multicam so I can't help you there. Generally you want your cameras to share the same format specs when using multicam. That is, frame size and frame rate. If you mix file types you might have to transcode everything to a standard format. On a Mac that would be ProRes. Multicam doesn't like differing frame sizes and frame rates.

Alternately you can leave the differing file types alone and layer the cameras on the timeline, in sync, and cut away shots you don't want. I do that on occasion when I get footage that multicam in Final Cut Pro won't sync up for some reason. I put the default camera (usually the one with the best audio) on the first track and the remaining cameras as overlays.