Is it painful as your muscles atrophy ?

Often not: Muscles can often atrophy without any accompanying pain. However, as weakness ensues, risk of painful falls and fractures dramatically increase.

It can be: Is it painful as your muscles atrophy? Yes & no. Atrophying muscle does not become a local pain generator, but the opposing & symmetric muscles become mechanically stressed, strained, hypertrophic & painful with chronic spasm. This phenomenon, called "crossed muscles", is common in Fibromyalgia & causal of the widespread regions of chronic pain characteristic of that syndrome; see comments below:

Maybe: Muscle atrophy by itself is not usually painful. If the cause of atrophy is a pinched nerve, then there maybe significant pain involved. Also, of atrophy affects function of a joint, then it may cause pain when you user the joint. Also, the weak muscle will tire out sooner and get sore from overuse more quickly.