You have to use the AFMC portal ($500 fee to access) and apply though there. Each school is slightly different but there is now one universal health form to fill out (titers, PPD, etc...) so that makes it easier. Depending on the application itself, the fee to apply can be $150 (Manitoba) or $825 (Queens). Timing of applications (whether they're accepting applications up to 16 weeks prior to start date, or within a specific time frame), duration, etc... also depends.
Go to the AFMC portal and most of it is explained there. You will also have to create a profile with the duration of all of your core clinical courses, med school, citizen information and such.