I'll start with the over-allocation question. In the old release there is no easy way to do this, but in v6 (which launched today) you will get a warning when you assign a task that will over-allocate the resource and even get an undo option.
As for the calendars, there are a couple ways to do this. You can either set the resource availability to 69% (5.5h/8h) for new projects. This will default their units to 69% so anything you assign them to will assume that they will not be able to work a full work-day on it. This is typically the route I would go, but you will have to update existing projects since this setting only applies to new projects (tasks that are already assigned would also not be touched). You can also change their physical calendar so that they can only work 5.5 hours per day, but there are some drawbacks here. For example, if you one day would like your resources to report time on these support activities as well as projectized activities, the data would be skewed with a 5.5 hour day instead of an 8 hour day.