First of all, did the helper signed already when you signed? If not, the contract has to be sent to her for execution before processing.
Secondly, did the agent submit to Immigration? Some agents may not do the submissions every day and will wait for a big lot.
If the contract is signed by the helper and the agent submitted to Immigration, you should have rec'd the ref number a week after submission, even you did not submit all the supporting documents.
Why it takes that long? Is your agent has its own office in Manila or it just works as partnership with agents in Philippines which supply helpers to a number of HK agents?
Otherwise, the agent should have the helper signed the contract already. It takes all-in 8 weeks to have the visa approved.