We are an Armed Forces family (RN), and have done the following.
From when ds was born (1995) until 2006, we did a mixture of weekending (thankfully the sea time was over), and when dh originally was appointed to Brussels, we six weeked it (long way from Brussels to Cornwall, whichever way you do it). I taught and ds went to prep. We coped.
In 2006 when dh had been here two years, he was told that he had another appointment out here until 2010. We considered leaving ds at prep and boarding, but he wanted to come to Brussels, so he has been at the BSB since 2006 and is now in Year 8. The aim is to stay here until 2012 when GCSEs are done.
I am a forces brat and went to several different primaries when I was young. I found it hard to fit in and make friends once the cliques had formed and I arrived after that, and it was always hard to leave your friends and start again at a new school.
If your postings will be in the UK you have the hassle of trying to sort out an MQ and a school, and not always as you recognise getting a good school. I know one lad at the prep ds went to whose Dad is in the Army in Germany and sent him to board in Devon precisely because of this.
As I don't know if we will be able to stay out here beyond 2010, I am having to start researching boarding schools soon, as I will want him to go from year 9, so he is settled and had time and space to choose his options.
The responses on here have been sensible so far, but you may get the very anti boarding school brigade on here soon, who don't necessarily understand the pressures on Forces families. May I suggest you post this in Forces Sweethearts, as there are several families from all three services in your position on that particular section of the board. Many of them have been there, and can give you good advice and recommend schools as well.
Hope that helps. It seems to be your marriage or your kids on occasions with the Forces!