If your company wants to switch from a legacy system to some new solution, which will handle your operations more effectively, you need to devise a step-by-step transition procedure. First of all , you need to prepare a PCI compliant environment for development of the new system. Second, you need to carefully study existing integrations with payment processors and front-end platforms, and decide, which ones have to be migrated to the new system. Third, you need to analyze your business processes, decide, which of them are already implemented in your system, and find out, which new logic has to be implemented in the new system in order to make it more functional. And finally, you need to devise a strategy for merchant, recurring billing, tokenization, and, if necessary, transaction data migration.
More detailed description of each of legacy system replacement phases is available in the respective article on Paylosophy.