You can still upload the old way, that's fine. You just won't be able to fully take advantage of the new file format, but it might not be necessary anyway. You also will need to be careful about the FPP version on each FPP instance, but if you update them all to 2.6, that's not a concern.
By default now, (settable) xLights saves fseq files in the new format. If you do a batch render of your show, you should see the size of your fseq files drop dramatically. My show went from 11GB down to around 400MB. Thus, if you upload those the "old way", you will be able to transfer them there MUCH faster than you used to be able to as they are a lot smaller.
FPP Connect takes it even further and creates optimized fseq files specifically for that remote. If that remote doesn't need the data for you P5 matrix, for example, it removes that data. Thus, the files that are sent to each remote is MUCH MUCH smaller. It also uploads them to ALL the remotes at once so you don't need to go back and do that.