I believe somewhere the tutorial taught about military units in 'free roaming defender mode', this can apply to economic units as well.
In case it didn't:
when you execute a move order while holding down v, the units will engage anything on the planet they can engage. Military units set to FRD on a planet you own become sort of a defensive group - they will always move to engage any hostile units on that planet, then move back to where you told them to be. Engineers, when placed in FRD, basically is the same - if they can do something, they go and do it. Then they return to the spot where they were issues the order.
There is a setting for warnings if there are hostile units present on planets, but not for directly being attacked, other than the normal attack/sound for a command station being attacked.
if you look in the ctrls button (bottom left), on the single planet screen, there is a 'alert when number of units present'. this will put a notification in the top left of the screen where wave warnings etc appear whenever the conditions are fulfilled.
There may be an autosave, but depending on your saving habits... Personally, I never overwrite saves in a game of this magnitude, for instance. There are some counters to bombers, but most of them require more than a minute of setup time (or a great deal of resources)
it seems the major source of agony is the warp gate raid section, is that by chance what you are up against?
You can never issue move orders to a specific place on a different planet, except the command station/rally point. Slightly more in depth logic:
you can order moves and attacks freely within the system the units are in fine.
you can order a move to another system
you may not order a move to another system, then an attack (or move within the local map)
Thusly, the 'best way' would generally be to open the galaxy map before selecting units (you can move units around via the galaxy map too). Say, I want to get my first group from point a to b, but I'm looking at c.. press tab, the galaxy maps opens, press 1 to select group 1, order move to b with right click.
You can only ever select units from a single planet at a time with this method, however, but that is often not an issue with ctrl groups.
