We actually sealed our seams before even compounding.
Here's our "seams first" reasoning - just our logic, not everybody may agree. We scraped out all the old, cruddy sealer with popsicle sticks & mineral spirits, then compounded just the seams, cleaned them really well - again with popsicle sticks & mineral spirits, then resealed them with fresh vulkem/parabond. For awhile, our trailers have had just the seams polished - which looks kinda goofy, but cool at the same time. Then we went back and compounded (and eventually Cyclo-Polished) the rest of the trailer in the end.
We've done this on both trailers and feel that it makes sense for a couple of reasons. If you leave the old sealer in place while polishing then reseal afterwards, the old sealer can chunk out and get imbedded in the buffs which causes undue scratching. By doing it this way, you can get the seams buffed up really well, then sealed which leaves the sealer cleaner in the end. If you seal first w/o polishing the seams - the polishing compound gets gooped up on the new sealer because we are trying to get the 55 years of oxidation off and working the area harder.
As we've worked on the trailer, we would take things off, then polish around the area before putting parts back on. This way, the hard work is done around all the details, seams, joints, drip caps, etc. and just the flat parts are left. Yes, we still will go over those areas again, but it'll be a touch-up, not the original cut, so the compound isn't as big of a deal.
Since you have already compounded, I would do the seams now. That way you can go back and touch up any areas that might get scratched while sealing before you Cyclo-Polish. Then Cyclo the whole trailer...
Just my 2-cents...