I think I'm understanding you correctly. You have an integration script from FDM Classic and you're looking to re-create it in FDMEE.
Sounds like you will want to add your code to the BefImport event script (using either Visual Basic or Jython). The script will capture the data from your relational source using SQL and populate the Open Interface table.
In the FDMEE Admin Guide, see Working with Open Interface Adapters and Using Event Scripts for details. There will also be code snippets for writing SQL.
Will I be able to use the same code from the integration script if using the VB route since the integration script is already in VB?
You can leverage some of the code, like the standard VB commands, but anything using the API will be need to be re-written. The FDMEE API model is different from the FDM Classic API model.
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So what if we have mutiple integration scripts, one pulling data from SQL server and another pulling data from Oracle server and there are variations of the SQL statement (different entities, currencies, etc.). BefImport restricts us to write only one script. Can you write multiple integration scripts within BefImport that pulls data from various ERP systems on SQL and Oracle and have different SQL statements?
there are couple of options here.
Do you feel comfortable with ODI? instead of using BefImport Script you can use ODI to populate the interface table by changing the Open Interface Project.
In ODI you can easily manage multiple flows and physical connections to heterogeneous source systems.
If you still want to use BefImport Scripts, you can create individual BefIMport Scripts (Ex: BefImport_Source1, BefImport_Source2...) and make the main one (BefImport) to use them based on location or any other parameter like data load rule.
In Jython, you can import custom modules within other scripts.
I blogged in the past about it: akafdmee.blogspot.com/2014/08/tips-tricks-using-external-py-modules.html
This can be useful as starting point.