Is there any requirement in the FMLA that the ee has to be able to perform the essential functions of the job as there is in the ADA?  If someone is scheduled to work 5 days a week but has certification that flare ups to a condition (life long) may cause them to need to be absence once a week for a full day, but they are the only person that performs this duty that takes 3/4 of every day, and no other positions are available for transfer that would better accomodate the situtation, what are our options.

This sounds like this is an ADA issue that you have to look at.  To be honest, I think consulting your attorney is probably the best move you can make in a situation like this.

You have an ADA obligation but, also, if FMLA applies to your Company, it sounds like the EE's condition is qualified.  You will need to look at both, which means transfer is a last resort, especially until you get this completely straightened out in terms of responsibilities under both laws.  Is the EE's condition the result of a job related injury?