Rough Patches Normal After Phenol Peel?

The recovery from a phenol peel varies depending on the depth or penetration of the peel into the skin.
Most patients are resurfaced by 10-14 days. Redness after the peel can last for up to 2 months. Once again, the deeper the peel, the longer the redness.
The bumps you describe, should be looked at by your doctor to make sure they are not scarring. They may just be residual areas that have not completely resurfaced with new skin.
The coverup makeup is easier to remove once you are completely resurfaced.

Healing depends on the depth of the peel and this is dependent on the concentration used to perform it.  Usually a peel takes two weeks to resurface the treated areas and two to three months  to regain its texture.  The redness that follows a peel can take up to 6 months to fade.  You are only two weeks post treatment.  I would suggest you visit your treating physician and give yourself some time to heal.