UPenn Score Choice

Does it matter for UPenn if I only self-reported 3 Subject tests on my Common App but using CollegeBoard I submitted all 5 that I took?

no

I am a bit confused about subject tests - I understand I need to report a full history of SAT/ACT tests (I have taken both.) However, subject tests are optional? I already took two subject tests and I was not pleased with the results, so I plan on retaking them in January. Do I need to submit my two poor subject tests?

Yes you need to report all subject tests as well.