Just add linearly SLR rate with your downstream boundary, like time series tidal water level. If you are using tidal constituents, make a time series with your tidal constituent and then add the SLR rate. I hope it will work in your case.
I have the same question on how to add the SLR to the simulations. What mention Jakia sounds like a good idea. You make your time series from the tidal constituents by doing the armonics sum (the sum goes from i = 1 to your N number of harmonics):
Water level = sum ( Ai * sin(wi*t+phasei))
where A is amplitude, w is the harmonic frequency, and t is time.