At what point in the skinning- fleshing- washing - stretching- tanning would I sew uh oh holes in my hide? (First time trapper and first hide)

I prefer to sew after fleshing before washing so the hole does not get bigger.
Usually only sew holes bigger than a .22 cal.

If you are going to sell the raw hide sew it just before you put it on the board after fleshing and cleanup.
If you are tanning it,do the same but you dont have to be as fussy with the sew job.You just want it to hold together thru the pickleing and tanning.This will keep the hole from getting bigger.It will open up when you are finishing the leather side when sanding off any bloom,but that doesnt matter because you will be going over the skin after it is finished tanning and cutting out all damages(like your sewed hole,clips in fur etc) and repairing before blocking.This will keep your repairs to a minimum.
A bigger hole left unsewn thru the tanning process will mean a much bigger repair(and resulting loss of sq inches)before blocking.This does not apply to small holes(size of 22 bullet) which can be left to repair when blocking.