Its possible to use the way that you prefer, but in my personal opinion to organize better your programs/projects I’ll recommend a repository for each program.
To help you better there is also the Atlassian Bitbucket documentation as you can see on the following link:
I hope this information could be useful.
I'd also prefer a repository per program to a repository per project. This will mean a (potentially) lot of smallish repositories instead of one (potentially) gigantic repository. As we don't know the details of your project and programs it's impossible to say for sure which way suits you better.
Because Bitbucket is missing a way to group repositories I've implemented a simple repository naming convention:
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