OK, stop and re-think this for a minute. First of all, you don't have to be residing in your home country in order to be eligible to apply through that embassy. You always have the right to have your application processed through your home embassy, regardless of where you are staying while the ap is processing or what your status is in that country (including Canada). That said, you have to figure out whether or not applying through Manila is in your best interest. Yes, any inland application you file will be delayed - maybe for a couple of years - because you do not have valid temporary status. But, as you said, your child is in Canada and is going to school - and that's an important consideration.
If you apply through Manila: the current processing timeline for spousal cases through Manila is up to 9 months. That's after the case is transferred to them by the Case Processing Centre in Mississauga. They first assess the eligibility of the sponsor - that takes approximately 4-6 weeks. If an interview is required (and you can influence this by the quality and quantity of the evidences you send with the application in support of your relationship) you will have to attend at the Manila embassy. It is likely you will not get back into Canada as a temporary resident after leaving to attend this interview - which is mandatory. Also, at some point they will request your passport, and you will have to take it to the Philippines - you will not want to mail it to them - so at that point you're stuck until they finalize your case and issue your PR. Some embassies ask for the passport early on during processing - others don't ask for it until they are ready to issue the visa.
At any rate - it would be faster to apply outland and just get this over with . . . get your status and move on, even if it means some time separated from your spouse. But, because of the child, do keep in mind that you can remain in Canada until such time as you're requested to either attend an interview or submit your passport. You will need to use the address of a family member in the Phils as your residential address on the application, but you can use your Canadian address as the mailing address so that all correspondence from the embassy comes to you in Canada. Maybe this way you can get the application in process immediately, and still allow your child to at least finish out the school term before you have to go back . . . and, hopefully, once you have to go back, it won't be that much longer until things are finalized and you can "land". And yes, it's okay to have your medical done in Canada. Again, stay until you have to go and be sure to use the Canada address as your mailing address so that you get all correspondence from Manila right away. Hope this helps.
