Before going too far, you'll want to check that the IR Codes that you have actually work correctly via SQBlaster.
The easiest way to do that is to create a Scene using one of the Channels of your SQBlaster. This will either be the primary channel, or one of the AUX ones if they've been wired up with an IR-Emitter (that's close to the Skylight)
In Vera's Scene creation dialog, select to create an Advanced Scene (varies by UI version), and select either the Parent SQBlaster Device, for the puck itself, or one of the SQBlaster Aux Devices, representing the IR-Emitter that you've attached to the Puck.
Next, select the Action of "SendProntoCode", and you'll be presented with a field that you can use to enter the ProntoCode that you've gotten.
Add, and Save this scene.
Now Manually Run this scene, and the Puck will be notified to send the IR/Pronto Code. If the Pronto Code you have is correct, and the IR-Emitter is "close enough" to the IR-Receiver on the Velux, then this should open, or close, the Skylight.