The only files that belong in the Tools folder are the ones that ship with SketchUp itself, or are given as extra tools by SketchUp.
ALL other files should go into the Plugins folder, or into that script's subfolder, which itself goes into the Plugins folder.
The basic [current] setup is that SketchUp auto-loads all .rb/.rbs files in the Plugins folder and then those in the Tools folder. It uses a system global-variable called $LOAD_PATH which is an array of the paths to be used for auto-loading. There are some special scripts that add new folder paths to this, this means that you can then auto-load files from elsewhere. Ruby can 'load' scripts from anywhere: if you just give the file name it looks in the folders in $LOAD_PATH, if you give a full path name it loads that specific file.
Because of this it's a good idea for authors to add flexibility into there file/folder 'path' coding, so that the subfolder of support files only needs to be located with the auto-loading .rb file for these other files to be found with it and also loaded in code.
Some older scripts mistakenly say to install into the Tools folder.
Unless they are specifically hard-coded to expect to be in Tools using them all within Plugins as outlined above should also work...
This tool's author is mistaken in his recommendations.
Putting the script into the Plugins folder [keeping files within the script's subfolder etc] should work fine, and obeys the basic principles used by every other author around.
I have the 'loader' ' SoapSkinBubbleTools.rb' in my Plugins folder - and its subfolder of files in there too.1.PNGIt loads just fine as an Extension, and once activated its toolbar can be activated successfully too...