yes there is a specific way.
basically, you want to have 2 of the 3 dots on the front of the camshaft facing upward (toward the sky) and the third dot facing OUTWARD, towards the wheels on the car (intake side towards driver's tire, exhaust side towards passenger tire). but the top 2 dots should be parallel to the ground.
here is a picture describing it... the top most picture on the page.
http://www.cygnusx1.net/Supra/Library/TSRM/MK3/manual.aspx?S=EM&P=52
also, there is a specific pattern that you should follow when torqueing down the bearing caps. this can be found in the TSRM, and it is on the same page as the picture i just linked you to above.
and another also: there is a difference between the intake and exhaust cam. the exhaust cam has a gear at the front of the camshaft that mates to the CPS. it is unmistakeably different from the intake cam.