Yes, I have seen the tutorials. They leave out crucial steps. That's why I am asking questions on the forum.
I do my puppets in Photoshop. If that is what you use, I can give some basic steps. But any specifics would really depend on the details of your puppet setup.
For the puppet I am working on, the artwork was originally done in Flash and each layer was exported from Flash and imported into Photoshop. (I do all my art in Flash, whether it will wind up in Character Animator or in Anime Studio, so they retain a consistent style from shot to shot).
I properly labelled my layers and the puppet, so far moves and talks when I move and talk, but:
1. I left the arms off the body because I didn't see any layer in the hierarchy for arms. Do they go on the body layer?
2. I need to add some floppy or at least bendy ears to his head (kind of like the Bunny Guy example)
3. I need to add a bendy fin on the top of his head, like the fish example.
Can I just individually replace layers, or do I have to go back to Photoshop and replace all the layers?
I wish this program was like most other programs where you could just drag and drop some artwork. It is not user friendly.
If you're starting off with an artwork file (such as a template PSD file) that you make a puppet from it by import the file, it's best to replace/add any layers in Photoshop so that any changes you do are automatically synchronized with your puppet in Character. You can still add additional handles in the Puppet panel, and those will be retained if you later need to modify the artwork structure.
If you start off with a blank puppet and open that in the Puppet panel, you can drag other puppets or artwork files from the Project panel into the Puppet panel and set up the hierarchy, but you would need to add handles for Fixed, Mousetrack, etc. manually.
Regarding your questions:
> 1. I left the arms off the body because I didn't see any layer in the hierarchy for arms. Do they go on the body layer?
You can put them in the "body" group if you want. If it's a layer Character doesn't recognize, it won't control it directly. However, if they are part of the warpable skin (rubber sheet within each puppet) controlled by something else, then they can move.
> 2. I need to add some floppy or at least bendy ears to his head (kind of like the Bunny Guy example)
For the things you want to bend/flop separate from others parts of the character, you'll want to make them their own subpuppet with Warp Independently checked (done in the artwork file by placing a "+" in front of the name, such as "+left ear"), then add Dangle handles inside that subpuppet above the areas you want the Dangle behavior to sway. You can also add "Dangle" to the name of the subpuppet (e.g., "+left ear Dangle") so that the center of its bounding box also dangles.
> 3. I need to add a bendy fin on the top of his head, like the fish example.
This should be similar to Bunny Dude's ears in that the fin is a subpuppet that warps independently, and contains Dangle handles in it that affect the swaying.
If you'd like to share a screenshot of your work so far, or the artwork file itself, we can provide additional guidance. Thanks.