From: Los Angeles
This is where the "Iso-Base" feature comes in really handy. If bases are not isolated by enemy AZOCs (Air Zones Of Control), it's usually not necessary to supply them. If they have no troops or aircraft, there's no real need for supplies. If they do, however, you want to make sure there are sufficient fuel and supply levels to keep your land and air units functioning well.
As for putting garrisons on far-flung bases, it's usually a waste unless you anticipate being attacked. The exception is if the bases has favorable terrain for airfield and port construction. (Level 6 is best with version 3.2, followed by levels 3, 5, and 7.) If you have spare engineer or SBF units, place them at the base along with at least 1000 units of supply. Even if you never end up basing aircraft, every extra point in airfield and port size is Victory Points in your bank.
Loading oil manually is also not necessary unless the base is isolated. Check out the oil level at the bases you suspect by pressing the F6 key. If there is NOT an asterisk by the Oil level number, the Routine Convoy system is failing to pick up the oil, and it may be time to form a convoy of AO's or TK's to get that precious oil into your economy.
When you have the supply system mastered, I recommend picking up fuel from fuel-rich bases such as those on Java, and bringing it back to the Japanese Home Islands. This may save having to draw Oil from the National Oil Reserve and refine it into fuel.
Civil war? What does that mean? Is there any foreign war? Isn't every war fought between men, between brothers?