My impression is that there is currently not provision to specify a particular FLWM desktop for the window of a X application. Whilst the '-display' option is supported by most (if not all) X apps to allow the selection of a specifc X server (but honestly how many users will run more than one), no such thing appears to be available for the selection of a specific FLWM desktop.
I only had a fairly cursory glance over the FLWM sources and could not identify a way to change the "desktop" value for a given "Frame" via a method external to the 'flwm' (or 'flwm_topside') process. I guess it would be feasible to create such an interface and a wrapper to start X applications that signals the target desktop to 'flwm', but I imagine that would be a fair amount of effort for fairly little gain.
Mind you I could be totally wrong, since I did not look to much into it.