After creating the .bash_profile and adding the export Path, should the path just be "Users/Folder/folder/bin" or not include the bin. I can't seem to run the connectiq command from the command line.
The programs you want to execute are in the bin directory, so you want the bin directory in the path.
As Jim indicates, the Eclipse setup is probably the simplest thing to do. Using the command-line is not a great idea if you're not already familiar with using the command line.