Question: I have children of various ages, and it is often difficult to have them wait six hours between meat and milk. Milk is an important part of their diet/lifestyle (including before bed), and eating disorders concern me.

Answer: There is near consensus on the basic principles and only small differences regarding their application to common cases.
Waiting six hours between meat and milk is a double-level stringency. The gemara (Chulin 105a) talks of waiting to the next meal to eat milk after meat. It implies that it is the proper way to be extra careful to avoid eating milk and meat together, and failure to do so may not be equivalent to eating a Rabbinically forbidden food. There is a machloket among the Rishonim if it is sufficient to finish the meat meal and take steps to ensure there is no meat in his mouth or whether one has to wait the normal time that exists between meals (see Beit Yosef and Darchei Moshe, Yoreh Deah 89). Sephardic authorities ruled the need for six (or so) hours, while significant Ashkenazic opinions required just to finish the meal or wait no more than an hour (see Rama, YD 89:1). While the prevalent practice of observant Ashkenazim is now to wait six hours, this may be more of a stringency than a clear ruling (see Chelkat Yaakov, YD 16).
The consensus of poskim is that under the age of three, when a child is too young to be significantly educated in religious matters, they do not need to wait at all between eating meat and milk products (they should not be fed them at the same time at any age). Although we generally accept the opinion that forbids "feeding" a young child Rabbinically forbidden food (Shulchan Aruch, Orach Chayim 343:1), waiting between these two types of kosher foods is not included (see one of the explanations in Teshuvot V’hanhagaot I:435).
After age three, children start becoming capable of following halachic restrictions, but their ability to keep some of them remains a factor. There is a concept, arising in several contexts (see Rama, OC 325:17), that the physical needs of a healthy child are halachically equivalent to the needs of a sick (non-life-threatened) person. For this reason, the halachot of even partial fasting on Yom Kippur begin only at age nine (Shulchan Aruch, OC 616:2). While waiting to eat milk products is not the same as fasting, a full-fledged requirement to wait six hours can compromise a young child’s well-being, especially those whose eating patterns are inflexible. Regarding the sick, very prominent opinions allow eating milk an hour after meat, after cleaning the mouth by eating and drinking (Chochmat Adam, 40:13; see Pitchei Teshuva, YD 89:3), including Sephardic poskim (see above; see Yalkut Yosef, YD III, p. 395 in the name of Zivchei Tzedek). Thus most poskim are equally lenient for children, at least under the age of nine (Chelkat Yaakov, ibid.; see Shema B’ni 54). Many take the pragmatic, graduated approach that the number of hours increases over time (ibid., in the name of Rav M. Feinstein; Teshuvot V’hanhagot, ibid.). Yalkut Yosef (ibid.), while legitimizing leniency even for Sephardim, limits it to eating nutritious food at meals, not to indulging in milchig treats.
The Chelkat Yaakov posits that keeping six hours is a minhag and as such should not apply to children under bar mitzva, but he stops short of practical leniency to children over nine. Yalkut Yosef contemplates leniency until one year before bar/bat mitzva.
A parent should use common sense and fine parenting skills in applying the general guidelines provided. The laws of chinuch (lit., education) have a formal element and a pragmatic one of how to best raise a specific child under specific circumstances. Maturity and demeanor are among the changing variables. In the face of potential eating disorders, some which can become grave, it is possible to be very lenient, and it is good for a family to have a wise rabbi they are in touch with. This forum does not enable giving advice regarding identifying real health concerns, including eating disorders.