The first run through is creating the initial load of the QVD so you can then going forward perform incremental loads. It'll take the most time to run but offers amazing performance load gains afterwards.
What I've done is create a schedule for the initial load 1 time in the QMC in the off hours period (4:30 am lets say) and it's done and ready.
Another tip I use is an if and do an if file not exists check and do the initial qvd genetaion else do the incremental load routine. Helps when passing through the Dev Test Prod environments and automatically sets up the initial load QVD and future incremental loads in one pass.