Not everyone using Methotrexate loses their hair or gets relly sick though there is usually a term used for Methotrexate days called 'M' day. Essentially 24 hour or so after injection can include some downtime. It may be gentler on your system compared to the long term effects of prednisone.
Also, re: cellcept - is there a reason why your rheumatologist did not want to try methotrexate first? If cellcept is believed to work better for you, is your doctor unwilling to write a preauth and petition your insurance company in your favor?
Some of the methotrexate users on the forum have experienced and overall improved quality of life with methotrexate injections vs the pills but I'm sure some metho users will chime in here shortly.
I do recommend you pick your 'M' day to be on a day where you don't have anything planned.