Last September we did Phnom Penh and Siem Reap with girls 11 and 13, and I really feel that yours will have a great time just doing what you would want to do. We travelled to Phnom Penh by bus from HCMC and stayed in the Hotel Asia, which is right in the middle of town, and very good value for money (if you're prepared to bargain): we got a room for the four of us with a great view of the main street from the balcony, for $15 a night.
The temple comples in Phnom Penh is easily walkable from the hotel, and, even if you're not crazy about templers, this is certainly worth a half-day of your time. We took a tuk-tuk from there to the High School/Concentration Camp, which is a "must see" regardless of your age, and from there walked back to the Asia. A couple of blocks befor we got to the Asia is a shopping comples with several interesting fast-food booths, and the kids really enjoyed this: a bit like being at home, but the food and drinks just exotic enough to be an experience.
Just around the corner from the Asia is tha main market, and this is another place which will open your kids' eyes. Our elsedt stiffened up as she entered, and looked like she was going to either run or faint. Skinned and headless frogs still breathing, baked spiders and grubs, fish and birds being gutted and prepared for sale.... it's all quite a heady experience for an Australian teenager (the younger took it all in her stride). AFter a few minutes, however, she started to relax, and by the end of the morning we knew that no matter where we went, we could visit the market again without causing her stress. Now she talks about it as one of her favourite experiences!
We travelled to Siem reap by bus, also. At the Long LIve Angkor Wat you can get two double rooms for $6 each, so accommodation is hardly a burden! We chose to do Angkor for two days without a guide (just a driver who took us across in the morning and met us each afternoon, at a cost of $3 a trip), using the excellent book which is on sale everywhere. There's lots of walking to do, but you can take tuk-tuks between the main complexes. BY the time we got to Ta Phromh, we realised the advantage of having kids with us.... they make friends so easily with the local children. Three eleven-year-old girls attached themselves to us and showed us around the village -- their swimming hole, their homes, their school, and the temple with (they said, wide-eyed)"ghosts". They made little garlands to give to our girls, and we took dozens of photos, and this, also, became one of the best memories our daughters had of their trip to Cambodia. And we didn't do an organised trip in the whole two weeks.
There's nothing much to do in Siem Reap itself, except (of course) to visit the markets.... by the way, children under twelve get into the Angkor temples free, so do NOT, regardless of what anybody in town tells you, pay for a pass for your youngest (we were badly advised, and had to argue with the gate man when we arrived -- showing him the passport to prove our case -- to get our forty dollars back).
Have a wonderful holiday!