how to help her 3 year old that is afraid of anything bigger then her?
take it slow and start with the smaller things first.
Meet "people" characters before the suited ones. Like mary poppins and cinderella instead of buzz lightyear and woody. Meet the people characters first and slowly warm into the others. If she freaks out, don't take her to see those.
Start on the small outdoor rides first. Go on the teacups, cinderellas carousel, poohs playful spot, dumbo...etc. Then go to the bigger not scary ries like winnie the pooh, it's a small world, the jungle cruise, see how she does and then slowly move into the bigger rides.
how to help her 5 year old with epilepsy and keep him safe?
Seek a doctors advice, go slow, and let him be a kid. Obviously the same rules apply, you have to keep your eyes on your kids.
which rides her kids would be comfortable on?
See above
and what are the opions on the downtown disney resorts?
I have no idea on that one. I've only stayed within the parks one time in the past.