The Stress Coat won't affect the treatment, no.
However... I say this to everyone treating for Ich - you don't need to medicate. Maracide and other medications will succesfully treat ich, but their side-effects can be worse than the original ailment. Salt is, IMO, a much better method of treatment because it effectively eradicates Ich, without any side-effects.
If you do decide to treat with salt, do a large water change to remove as much of the maracide and parasites as possible, then add 1 heaping tablespoon of aquarium salt per 5 gallons of water, disolved first in a cup of tank water. Leave the salt in the tank for 2 weeks, then resume weekly water changes to eventually remove all traces of salt.
You're pretty well into your Maracide treatment already, so it probably won't be necessary and definitely not practical to start a whole new treatment... but just FYI
Anyway, all that to say, go ahead and add the stress coat! :P