I do this according to the instructions of my relaxer. Apparently while the cuticle is open, before neutralizing, the conditioner absorb into the hair easily. Not sure if this is any better than deep conditioning under a some dryer, but I enjoy doing it this way.
Adding to HoneyDew's explanation...a reconstructor containing protein puts the protein back into the hair cuticle that were lost or broken down during the relaxing process.
I've used Aphogee 2 min Keratin, I currently use Nexxus Keraphix.
Aphogee Intensive Keratin Reconstructor (Im gonna assume this is the 2 minute one everyone talks about)
CPR
and Generic Joico K-Pac
Next I might try the Ion Reconstructor, I love that one, dont even know why I strayed!