Unfortunately in the current version, the uTool project files are not compatible with the playlist editor files. For the uTool revision 1.0.1 we mostly worked on the stability issues and could not get this fix done. It is not possible to drag and drop folders to make uTool song projects in the current release. What we shall do however in the next release is to allow the user to import content from a drive or folder(s). This way your problem can be solved. The time frame for the next release should be within 2 months or earlier from now.
You are also right about the numbering of wave files. We shall fix that too.
Thanks for the time taken to report all the issues.