Maybe. Who makes the booking is not as important as how the payment is made and the terms of the rate. When you pickup the car or check-in to the hotel simply present your membership card and ask to have the rental or stay credited. If the rate is ineligible they will probably tell you, but nothing bad will happen.
I'd highly recommend adding in member numbers after everything is booked.
Much worse chance of airlines/hotels not giving the benefits one would earn if you wait.
OP - When everything is booked, simply add in your member number. Be it Alamo/National, Marriott/Hilton.
For airplanes - use one number for US/UA/CO flights or others in the *A.