SAP FI is Financial accounting and SAP CO is Controlling(Management accounting)
You can always sit for the module that is comfortable with you. Domain experience do matter so
make sure your previous experience sits well with any SAP Module you want to go for.
To be an SAP Functional /Technical Consultant, you will need to understand the business processes
of the sector you are working in. In the case of SAP FI/CO, business processes/transaction that impact
the FI side and likewise the CO side, integration aspects and so on.
In the long run, you will always do well in SAP if you choose a module that you are comfortable with.