You'll have to do this for each playlist, unfortunately.

Actually there is another (better?) way. Go into the jemplode options and set "Tag name to sort on" to "tracknr" and check auto sort on import. Also make sure you have dedup on import checked as well. Now reimport all your tunes. They will all be dupes so you wont have to upload again, but jemplode will update the sort order anyway. Do a sync and you should have everything sorted by track number.

-Mike