Unfortunately this always ends up being a pretty manually intensive process. Within Marketo, you'll need to update the Acquisition Program after the fact through a smart campaign. Make sure to first set the Acquisition Program, then set the Acquisition Date (doing in the opposite order will not work).
The unfortunate reality right now is that when doing batch updates to leads for Acquisition Program, there are no tokens that will work properly, so you'll need to manually select the program in the flow steps. Acquisition Date will be able to use a datetime token (e.g. Created At, or SFDC Created Date).
I've seen other comments in the community mentioning that an API would potentially be able to bulk updates, but I can't speak to that personally.
Useful fields in Marketo for telling where a lead came from are the: Original Source Type and Original Source Info fields.