With open(1), you don't need the full path to your application, so...
open -a Project\ Builder
.. will work just fine.
And with BBEdit, you don't need to define an alias, just install and use the bbedit(1) command-line tool provided by Bare Bones. It includes a number of helpful switches for doing things like creating or printing a file, leaving BBEdit in the background or waiting until BBEdit is done with the file (so you can almost use it as an $EDITOR replacement).