some people (like me) prefer to wander and absorb - if this is you go with just the tuk tuk/car, if you prefer lots of detail and structure go with the guide - though I think that if I was taking a 5 yr old I'd prefer to go sans guide. Beng Melea is a great temple for the kids, lots of Indiana Jones type exploring possible.
in the top questions (upper right) - last dot point - is a good thread, though the little chap in this was in a wheelchair there is still plenty there which will help.
if you use the search box (directly above your post) and search for something like 'travel with children' (or any other phrase similar to what you'd use for a google search) you'll get lots more info - there have been a number of families who have travelled with similar aged kids.
do get a hotel with a pool - nothing spoils your holiday than hot tired cranky kids so it's good to be able to come back for a swim and something to eat which should return them to nice children quickly!
when are you going and for how long? and anywhere else in Cambodia? this will help people tailor their info for you.