Simple answer.
ask the UK Border Authrity on their helpline.
They are very helpful.. (No on application form)
or look on these pages with application forms also.
http://www.ukba.homeoffice.gov.uk/eucitizens/
http://www.ukba.homeoffice.gov.uk/eucit ... ropeanlaw/

Your problem will be if you have 1 passport.
You could enter any EU country at any time under the visa waiver rules (90 days).
If your passport is tied up with an application, you have no document to travel on.

I note that on the opening page (2) of EEA2 guidance notes state clearly,
"You and any family members included in the application
must be in the UK to apply."

So (in your case) enter the UK under your Visa Waiver rights.
otherwise you would have had to use your EEA rights to apply for a entry Visa to enter.

Note the application can take months to be processed !
so dont expect your passport back quickly...