Question about two tone and stripe painting

I'll be using Nason base/clear and am wondering about the masking for the top and rear stripe. I've been told to spray the base color then mask for the second color, paint, then spay the clear. I need to know if this is right and if so, how soon after spraying the base color can I mask it off. I'm worried about marring the paint with tape and paper. Thanks in advance.