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I am very new to quantum computing, so this might be a really simple question. I am coding a quantum computer simulator in python from scrach and I'm not sure how to make registers work.

I would just use a wavefunction which stored all of the qubits and when operations were needed to be made (for instance a Hadamard operator on some qubit), I would just scale the operator accordingly and apply it. This seemed to work quite fine, however now I need to implement a phase estimation algorithm, where two registers are used. At first I thought to treat them as seperate wavefunctions, but when It came to controls I had to combine seperate registers into one wavefunction. Finally, It shows to apply QFT and measure just the first register.

So my question is: how do I go about implementing seperate registers and using them? Is there a smarter way than just to have one insanely large wavefunction? I have no idea since registers seem to have to be interconnected for things like controls to work.

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