The advice I've been given is to put them in a phase 3 assault hex so if the opportunity to land them is available you can do so. Without the Hq units cannot get csp's which means they cannot attack from multiple hexes nor may they use support (arty or naval).
For your second question read 18.8.1 Allied Regroup Segment. It explains what to do with units who were not able to land. Basically assault units which couldnt land reform where possible and then must be landed in subsequent turns before any other units can be landed.