While flying, click the "Flight Plan" button in the lower left to bring up your flight plan. Find the waypoint you want to fly direct to, and click the "Direct To" button next to that waypoint.
I think this will delete the waypoints prior to the one you selected for "Direct To", so don't do this unless you're sure you won't backtrack.
Future waypoints will be preserved and will sequence in as normal after you pass your direct waypoint.
An alternate way to do what you want might be to grab your magenta line just before your desired "direct to" waypoint, and rubber-band it to your current location to add a new waypoint. I don't have my iFly handy so I can't test this, but I think the iFly will identify the segment between your current location and the next waypoint as the active segment, and you'll progress through the remainder of your flight plan as desired, but without losing the intermediate waypoints that you "skipped".