I recommend starting with the Symbols and Symbol Management chapter in the User Manual (accessible from the help menu), it explains the details of how to create your own symbol catalogs, and then how to import .png's (recommend reading the entire chapter, not just the importing png part inside it, since that part relies on what has been explained earlier.)

The Tome do go into greater detail about your options, but the User Manual should get you started.

For the second point, CC3+ scales to paper on print. The map itself should be scaled according to the actual real world size, not the print size, so if you wish to cover an are 500 by 500 miles, set the map dimensions to 500 by 500.

In the print dialog, you can then specify desired print scale when you print, or if you export to an image, set the desired pixel size as needed by your print.

When you save a custom pal, it saves a file called fcw32.pal in your CC3+ data directory. If this file is present, ALL maps that doesn't have an attached palette will use this instead of the default palette. So the solution is to delete or rename this file, and CC3+ will revert to using the default again.

Check that you haven't disabled Hotspot under Tools -> Options -> Links and Hotspot are active.

An additional thing to look for when things doesn't seem to go right is the number of selected items during the command. The command line will show the number of entities selected when you do the multipoly, and if you expected to multipoly 2 entities, but the selection tells you 3 selected, then that is a good indication that you have an extra entity in there somewhere, possibly a doubled-up one like here.