In TypeTool's Font Window, you can choose any encoding in the "Names" mode. An encoding is a plain-text file with the .enc file extension, where the first two lines have the format:
%%FONTLAB ENCODING: {NUMBER}; {NAME}
%%GROUP:{GROUPNAME}
Where {NUMBER} is any random number, e.g. 384782 (must be unique), {NAME} is the name of the encoding as it should appear in the dropdown list of encodings, and {GROUPNAME} is an optional grouping name which is used to group encodings if the Font Window menu bar is in the bottom position.
After these two lines, you just enter one glyph name per line, e.g.
a.smcp
aacute.smcp
agrave.smcp
b.smcp
c.smcp
d.smcp
The glyph names should be compatible with the FontLab Glyph Naming conventions. More information can be found on pages 89-101 of the TypeTool manual. However, I recommend downloading the FontLab Studio 5 manual for Mac or Windows:
http://www.font.to/downloads/manuals/FLS5MacManual.ziphttp://www.font.to/downloads/manuals/FLS5WinManual.zipand reading the section "Advanced Glyph Naming and Encoding" (pages 145-153 in the Mac manual). That section is omitted from the TypeTool manual, but does apply to TypeTool as well. That should give you more general insight.
Regards,
Adam