I think you are asking whether, if there are duplicates in the roll, if you should keep them together? I probably would not do that, myself.
My only complaint about the jelly roll race is that I don't care for the look when a fabric is too close to itself in the layout, but I don't know of any way to avoid this. Cutting the strips into smaller pieces (halves or thirds) would help, but it would also double or triple the work of keeping the pieces spread out.
Best bet is to embrace scrappiness and just start sewing. In my experience, the more you try to control a jelly roll race, the more frustrating it gets. I did find that I liked the quilt better when I used a square between the strips, but that's just me. I hope you have fun with it!
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