With syncronisation it is straightforward enough even with the blades attached.
A medium power ejection seat will cause the pilot leave the end of the gun at 60 ft/sec. The pilot and seat is about six feet tall so top to toe will take 1 tenth/sec to pass a certain point.
A 3 bladed main rotor turning at 240 Rrpm is turning at 9 blades/sec so if the seat is sequenced to fire as one blade is approaching the overhead the seat will be clear when the next blade comes around.
Should you have more or a faster rotor then part of the sequence would be to slow the rotors by whatever means to bring back the same time frame.
The advantage of ejector seats is that you can get rid of whining co-pilots.