I am having some tracking issues and I am wondering if I need to check off these little mystery boxes next to the ad tokens.
Can anyone explain to me what the hell these things do?

After a shit-ton of fucking around with CPVLab, I believe those append/pass that value onto either/both the Landing page and the Offer page...
I tried the LP check box once and clicked my ad and found the toke appended to the end of the URL where (at the moment i was using it) broke my link and gave me a 404 error....
Use the "LP" checkbox if you want to pass tokens or any other paramenter onto your landing page in a specific places/areas on your page. (dynamic insertion)
Use the "Offer" checkbox if you want to pass dynamic subids to your affiliate network. cpvlab will pass them on every click. don't forget to add the network subid token under the "URL Append" and the "Parameter" text boxs.