Not sure if Piskel exports TMX files. If it does you can load them in C2 editor. The tilemaps can be loaded from Json strings too, so if you see an option to export use it.
You can combine all the tiles into 1 sprite strip, without duplicates I know.
I picked up Piskel a while ago. a very fun little program.
Wish i had more information for you. I am sure others in the forum have piskel too, so maybe they have a workaround for you.