I'm assuming that you are talking about the rear flares, since if you are having problems with which side the front ones go on, then you have more problems than what anybody could help you with.
The rear flares are longer in front of the tire than behind. That should let you decipher which flare goes on which side. But, with a rugged ridge product it hard to say if they are made that way. Rugged ridge isn't exactly the "top of the line" company, and most of their products are made in china anymore, So you might just have to guess.
'87 YJ, 4.2L built and bored, 8.5" of lift, 8.8 rear, AX15/NP 231, Tom Woods drive shafts, Flat fenders, 12,000LB winch, Custom bumpers, Rattle can paint job. Never completed...