It sounds as though you are applying for a CPL with instrument and MEP ratings. If so, you don't need to fill in any ATPL froms. There is no such licence as a Frozen ATPL. It is an informal term meaning CPL/IR MEP ATPL exams passed and multi crew course completed. Your ATPL will come later when you have, among other things, your type rating and 1500 hours.
Yes, you do have to get the forms signed by your FTO and it's a good idea to have them sign your log book to confirm the hours. I think this is essential for the CPL application as you have to have 200 hours for licence issue. The only way around this might be to send the stuff to your FTO and ask them to send it on.
You talk about ball ache. Wait 'till tyou write out the cheque
AP