Where: When drilling, leave boot on foot to ensure correct positioning.
What size: Whatever size suits you best.
Not a contortionist? Ask grown-up to assist.
PS As with any question asked on the internet, it's a safe bet that it has been asked and answered before.
Why not have a go? It's free, or near enough. They should have charged; the inventors would have made a fortune. Type in the question and up pops the answer. Don't believe me? OK, let's go...
Google search of:
holes drill motorcross boots water The five basic words of your enquiry.
Reveals:
http://www.dirtbikeworld.net/forum/showthread.php?t=65730
http://www.advrider.com/forums/showthread.php?t=302365 Feck me, it must be possible even Ewan managed it (probably someone in the production team tipped him off) and it made a real impression on the dude.
I got bored after that but it will give you a taster.
Tell you what, to make life more interesting. Drill the fecking holes, stand in a river and then let the water drain out. But, before you start, take pictures of the whole process, noting drill sizes, positioning, riding to river, stepping in, stepping out, water draining out and end result. They will make it a sticky if it's well enough presented.