What exactly do I need to do to get the two to coordinate? I understand with the 2.0 release I would create a new product in limeLM and copy the .dat and GUID into the project. That guarantees that it won't work with any serials but the 2.0 serials.
Correct.
Then to deal with upgrades, do I just create a new FTP location for upgrading from 2.0 to 2.9? Using this method I would need new WyBuild projects for each major release. Is this optimal? I don't think having to uninstall/reinstall my product (going from 1.9 to 2.0) would be that big of a burden. Especially since they will need to put in a new serial number anyway.
Well, there are a few ways to do this. The easiest thing would by to release one last "1.x" release that offer a way to switch the "server" site where the 2.x updates will be stored.
Does that make sense? So a user could click "upgrade to 2.x", they enter a serial, they download the update, and they're running 2.x.