Academic letters they can upload themselves so it's not a big deal to wait. Also, you can remind them a bit later given that you have internet.
But don't hesitate to send (useful) reminders when you think it's appropriate.
well in my department, everyone interested completes the application and THEN they select ONE person. (Then the institution chooses national nominations). So a lot of time can be wasted on an application to be rejected at the departmental level...
the number of nominations they can do for that specific agency over 3 years
for instance, if the floating quota is 2 for CIHR, they could nominate one person this year and one person next year, but then 0 person the following year