I would always advise to write a cover letter whenever submitting something to CEM. Especially in this case - if you are just submitting the RPRF alone - there is no official form. If you are submitting the RPRF along with other documents, just attaching the check to the email will do.
In your case, I would suggest you write a cover letter (note - you need to always specify your File No. or UCI in any correspondence with CIC/CEM) - and state there that this check or proof of payment (bank draft etc.), in the amount of <Php x or $ x> is for the payment of the Right of Permanent Residence Fees for you, the principal applicant and your dependents.
IMHO, sa tingin ko CEM people have a lot of things already on their mind, sa dami ng applications to be processed. So better we say exactly kung ano purpose ng correspondence mo, at the same time, malinaw na reference yung file # mo para madali na nila i-process para saan (i.e.bubunutin pa ang file mo, aalamin kung ilan ang dependents, etc.) and then madali din sila mag decision saan na pupunta ang application mo, or anong next sa process sa application mo.
/hope this helps - and good luck to all....