Yes generally prescription Ibuprofen is stronger than the over the counter variety. It is not any different other than that though from what I understand. If you want to know more you can always call your pharmacist and ask they are very good about answering questions about both prescription and OTC drugs.
Find out from your doctor what mg's., he/she recommend's. They will also tell that if they recommend the 800mg's then you can take 4 200mg's., to equal the 800. If they want you to have 600mg's, you can take 3 of the 200mg's. You should get a dosage from the doc., first.