Having done a fair number of core repairs and re-done previous owners "drill & fills" I can assure you of a few things:
#1 Working from the TOP is the ONLY way to avoid voids!! It's called gravity!
#2 The water took years and years to penetrate and rot the deck you will NOT dry it sufficiently in even a month or more. you need NEW balsa!
#3 These "Ginsu" equivalent "penetrating epoxies" are BS!! Period and end of story! As I stated before it took the water years to penetrate that much core. Epoxy begins to kick in as little as an hour or two at which point it begins to thicken and or NOT penetrate!! Having cut open my fair share of "drill and fill" short cuts I can assure you the epoxy penetrates balsa all of about 1/16 of an inch if that!!
Try this experiment. Take a piece of balsa and drill a 1/8" hole. Now inject that hole with "penetrating epoxy" and let it kick. Now chip away the balsa around the hole until you find it solid and hard where the epoxy "penetrated" it. I've done this and I think you'll be amazed at the snake oil BS you've been sold!! Again, years for the water to penetrate but an hour or two for the epoxy??
Can you say "Ron Popeil salad shooter" ten times fast..
Unfortunately, there is NO easy way to do this job and going at it from underneath will get you a sub par repair unless you have serious vacuum bagging experience and remove the entire inner skin then completely rebuilt the lamination schedule for the inner skin..
Unless your deck is soggy at a key structural location like a mast step, chain plates or stanchions sail it until winter then tackle this job from the top..