Gerhard Ward at Fox Valley Off Road (www.megacross.com) always has a nice little loop put together for the 50cc bikes at his harescrambles.
As the father of a 50 rider there, I can say when faced with the question, make the loops longer rather than shorter and mix in some tight stuff. When you think you have the length just right, add another 20%. And if some sections look way too tight for a big bike, it's probably just right for a 50. Ward usually has some areas he needs reverse and a couple attempts on his quad to get through, but the 50s can zip right around.
Also, I wouldn't overdo it with numerous loops for the various skill levels. Maybe one section that the faster 50 kids go on that the slower guys on the PW50s, etc., do not.
Do have a few wider, open areas, though, so the faster kids can get around the slow guys with little trouble.
I think Ward does a 20-minute race for the 50s (or maybe it's 30?) Either way, it works out just about right. I wouldn't run them much longer than that because of over-heating issues on some of the high-performance 50s.
James