There is a bit of a learning curve to the site, not just for the DM but for players. I ran a game of Tiny Dungeon to record for YouTube and, even after the second attempt, I still don't know how to truly give players persistent control of their tokens.
The big thing I took away from it is a little command in the object menu called "convert to bitmap" or something along those lines. It gives you free reign to scale objects without them snapping to the grid which is handy for map tiles that don't quite line up. Once you're done scaling, use the "send to map layer" command to make it a map so objects and characters appear on top and can't move it around.
Otherwise, take some time before your game to watch the site's introductory and tutorial videos and just fiddle with it a bit. Have fun with it!