IMO the best way to do cardio is by time and by heart rate. Hitting level 6 on a machine will not do a thing if you are not pushing your heart rate into a zone that will burn fat.
Here is a calculator:
http://www.stevenscreek.com/goodies/hr.shtml
Bodybuilders have different theories on how and when to do cardio. Mine is NOT the normal routine. Cardio can eat muscle or slow gains but I don't worry about it because I am in pretty good tune with how my body responds.
I do cardio just like I used to train when I was running competitively. Personally I like doing cardio for 45 minutes at 80-90% of my max rate (usually throwing in intervals) three days a week and light cardio twice. Somedays, like squat days, I still need my cardio but hitting something intense will not work so I hit the bike at 60-70% of my max.
For example, yesterday I hit the elliptical machine. I did a 5 minute warm up, then cranked my heart rate up to 170bpm then did a 5 minute cool down. Today I did legs so I hit the bike for 45 minutes at roughly 140bmp. Tomorrow I will run for 45 minutes at 80%.
My greatest concern is maintaining my cardiovascular health - especially if I plan to continue to use AAS and other substances. Most BBers (well some - I cannot speak for all of them) do not place great emphasis on cardio - I do. My resting heart rate is 59 and I am in very good health (knock on wood!) which is pretty good.
I know the muscle on the outside is not worth a damn if I do not have a heart beating healthy on the inside.