You can only pay into one cash ISA in a tax year (6 April to following 5 April ). A transfer, provided done through the proper route between institutions, doesn’t count as a “pay-in”.
I don’t entirely understand your question, but I think I am answering what you are asking here.
If you have paid into “A” this tax year, you can transfer money from “A” into “B” and keep paying into “A”. You couldn’t put anything into B other than by a transfer until the nex tax year.
I am not an expert but did look into this from point of view of putting something from my existing ISA into a fixed rate fixed term ISA.