Wearing the shoe you intend to cover, drape the fabric over your leg.
If you’re confident in what you’re doing, you can use the actual fabric you’re making them with. Otherwise, find something with a similar weight / similar degree of stretch.
I find it easiest to do this on someone else / have someone to it for you, rather than do it yourself.
Whether doing it as a one person job or two, just take your time and pin it up how you want it to lay on your leg.
As always, make sure to keep the greatest degree of stretch going around the leg, not up and down.
I like to start with an initial "rough pin" to get the fabric roughly in place, and then adjust pinning as needed to work out any wrinkles.
Aim to get the pinned "seams" to line up straight up the centre front and centre back of the leg, and straight down the centre of the sole of the shoe.
(Note: I did this with no seam up the back, intending to cut it on a fold - you can pin all the way up the back for a more fitted seam)
Note: if you're using a full boot, rather than just a shoe: Be careful not to drape the fabric TOO tightly around the existing boot, or it could look misshapen when finished.
Also: You want to be able to get your foot in it!
Once you're happy with how it's draped, make note of any top edge locations or other areas of note - where you want a peak to be, where it should end behind the leg, placement for a design, etc.
Mark these spots with a pin or chalk/pen/etc.