Yes ISIS can generate a BeSS compliant fits spectrum. You can test your spectra at the BeSS website without actually submitting it to see if it passes. Submitted spectra are then examined by a human for quality before being included. Note that you have to sign up and supply details of your setup before submitting spectra.
The amateur Be star monitoring program was originally set up for high resolution observations to study the shape of the H alpha line profile. (The LHIRES III spectrograph was designed around this requirement as at the time there was no commercial instrument capable of sufficient resolution). If you are measuring targets which are too faint for high resolution or are rarely observed or if you pick up a significant change in any target (eg in EW or from absorption to emission or vice versa) even at low resolution, this would definitely be of interest and should be reported on ARAS/spectro-l forums and submitted to BeSS. The companion website ARAS BeAm details which stars currently need observations.