RTX 4090 into PCIe x8 slot

You have the X99-DELUXE correct? If so, yes it is going to matter where you place the GPUs The board's manual states that for 2 way SLI configuration the board

On the motherboard, PCIe lanes appear in x1, x2, x4, x8, and x16 variations More lanes mean more bandwidth, as well as a longer slot GPUs are usually

does it matter what pcie slot i use In general, as long as you are able to run your GPU at PCI-e x8 or above , you can expect

does the pcie slot matter for gpu If you do this on a B550 or X570 board you'll be limited to PCIe x8 bandwidth when using the RTX 3080 and that limits you to PCIe x16