the outputs need to match the inputs of the process, this is the only condition you need to observe, and you are then free to enter amounts for 1 or for 2 items. openLCA scales the processes automatically in the calculation so that every process delivers only what is needed to produce the functional unit that you specify for the product system, which means you do not need to worry about how much each process is needed for the overall model. E.g., you will also have a process producing 1 kg of woven cotton and link it here althoug here you only need 120 g.
I assume 'upper, lining & thread' is not yet the complete shoe, thus you could also just enter the amounts needed for 1 shoe / 1 item. In the end, you might have a process where the complete sneakers are produced, and there you could then say 1 pair of shoes is the output and the inputs are, accordingly, for 2 shoes.
Hope this helps!