How would one go about creating a SAP RFC that runs a transaction with parameters and return its data?
I have seen someone use a PERFORM BDC_DYNPRO and when I run the code through the debugger it seems to run the actual transaction screens. How do you go about setting this up?
There's plenty of RFCs in SAP systems that does exactly that - they're called BAPI functions. Filling parameters can be tricky sometimes and documentation for some of them are not really helpful. Take a look in transaction BAPI to see a list.
You can also create documents in transactions through code using IDOCs, that should be called using built-in IDOC RFCs.
BDCs are not really recommended for what you're trying to achieve, as they simulate the screenflow inside the system and that can consume a lot of resources for some simple tasks (like adding a new item to a document). BDCs also depends on positional references and that can be a pain to implement/maintain. BAPIs are always preferred over BDCs, however, in some cases you don't have BAPIs for a transaction and there's no other solution than using BDCs.
Finally, as I said some BAPIs can be really tricky to implement, so a RFC "wrapper" could be a way of simplifying the integration processes.