If you're going to do a frame for a known engine for which there are already other frames around...My experience is that you're best to make up a small subframe to act as a dummy engine. With a substantial reference point/bracket which goes on the swingarm pivot points to keep all in correct orientation. I find that it's best to add the motor mount points once the main tubes are in place. Could be different if it's a spaceframe with tubes ending at motor mounts though.
As far as jigging up goes, there are pitfalls. I was shown a guy's frame jig here which he'd made off a genuine early Rob North Triumph frame which wound up out here. He'd made a nice job of it but had made clamps for specific defined frame members rather than jigging the fixed points. Then once it had dawned on him the frame he had wasn't symmetrical it all unravelled, LOL.