You can't specify the location of an ibay during creation. SME server isn't designed to work that way.
ibays are by default created in /home/e-smith/files/ibays/
You can do one of several things:
Once the ibay is created, make one or more symbolic links from wherever your desired folders are, to the related ibay folders. Keep in mind that an ibay has the following folder structure:
myibay ->
/files (this is the directory shared by Samba)
/html (Apache 'publishes' html in this dir)
/cgi-bin (files in here are executable by Apache, via the url
http://servername/ibayname/cgi-bin/programname)
So, if you had a bunch of files in another location that you would like to share, symbolically link that directory to /home/e-smith/files/ibays/youribayname/files/
Likewise, do the same for any HTML or CGI-BIN dirs you might have.
If this isn't enough, then you'll need to look at creating custom templates to do the job for you.