We're still trying to figure out ways to make it easier to keep track of an expanding world, while not losing the core Hegemony concept of one-giant-continuous-map.
For now, set the middle alert tab, the one named, "Units, Buildings and Cities Under Attack", to auto-pause when anything you own is attacked. If you mouse over the alert, the check box to enable auto-pause appears...
When the game pauses, you can hit the "c" key to jump to the unit attacked. Repeated hitting "c" will cycle through all of your units, buildings and cities that are under attack. If you hit it once, you arc to the next site, which can help you keep your bearings. When you are comfortable with where the battles are, double-hit "c" to quick jump.
That way you can issue quick response orders to various situations and still focus most of your attention on more critical battles and campaigns.
The gameplay mechanics will be more refined in Rome. Rob is working on having reactive AI for your own friendly units, ideally with behaviors that players can choose from, such as, "retreat into city if attacked", "charge if attacked with ranged weapons", etc., so that you don't have to watch them so closely.
As to reinforcements and supply for an expanding kingdom, if you set up a supply network and protect it, reinforcements will generally take care of themselves. One often overlooked bonus, is to take advantage of healing shrines. When a unit is within the radius of a friendly healing shrine, supply lines are ignored and the unit heals as if it was in its home city. Another bonus is to camp a large army within the radius of a logistics shrine, to replenish their supplies.
Remember that when camped, a units view distance drops, so always keep a cavalry recon unit as a picket.