Is there a way to upload your own tokens? I can upload maps, but my monsters I have that are homebrew doesn't seem to transfer over. I can do it with avrae using critterdb. 

Also I couldn't get Targeting to work or to get them to roll saves or checks. 

When creating a homebrew monster you can upload custom images for it. These will show when adding monsters to the Maps tool.

There is no targeting system in the Maps tool. To have things rollable for the monster you need to ensure to use the rollable notation for monsters. See this thread for more info: https://www.dndbeyond.com/forums/dungeons-dragons-discussion/homebrew-house-rules/106856-adding-rollable-tags-to-your-homebrew-monsters-for