If it is part of the e-file requirement (e.g. send a copy of the federal with state) then it will e-file that way, normally.  

There are a few forms that cannot be e-filed and must be manually attached to the e-file return.  To attach a PDF of the form you want to go with the e-file return click the E-File menu button from inside the return you want to attach it to then click the Attach PDF.  From there you can choose what file you wish to attache.