Hi Ethan,
Instruction keys you can maintain in Vendor/Customer Master Record, general data section, and your question how we can accommodate by company code:
1. You can maintain Instruction Key in House Bank Master data, under Data Medium Exchange tab, T.Code FI12, which is company Code specific, in this way you can maintained company code wise different instruction keys. If the instruction key is not maintained in vendor/customer master data, then the default instruction key defined for the house bank is used.
2. You can also enter Instruction key at document level, in vendor/customer line item or it can be overwritten
Regards
Javed