Hey JD 
Unfortunately (unless it's changed recently), you can't use tokens to update the Acquisition Program field. Would definitely have its benefits if you could. For now, it does have to be at the SC level on each program. I tend to just build them into program templates as much as possible, educate my users on proper process as much as possible, encourage them to use check lists as much as possible, and then (because I'm the untrusting sort) have "check in" lists in the system to keep tabs on any leads that have that field blank, and try to correct any issues quickly before they scale to oblivion. 
This thread is a really useful one to bookmark on this subject: Acquisition Program Name and Date Not Automatically Set - esp. good to be aware of the points around Acquisition Program vs Acquisition Program Name.