If your [GC100] IR Devices are "registered" with Vera then the SQRemote app will pick them up, and let you map the commands to Buttons (etc). So it's possible, but a somewhat long-winded process to create/setup IR Devices within Vera (using the GC100 etc). Typically this relies upon Vera "knowing" about the types of [IR] Devices you use, as it has a fairly small catalog of Pronto codes, or "hand building" the device files (@strangely has posted an example in the forums).
Anyhow, it can be done, it just takes a long time to get them setup correctly - especially if you have a lot of unique IR device types. Ultimately it'll come down to how much you value your time. Personally, I use a combo of the SQBlaster and hand-built [MiOS] Plugins for my devices - both being controlled seamlessly by the SQRemote. In my case, my Custom Plugins control the devices over Serial, or Ethernet, and use the same [MiOS] Interfaces it uses for IR-based Plugins (which is why SQRemote can see them, since it looks for them within your MiOS unit)