Luckily a perk about being one of the bosses is a lot of free time
The world is split into 9 areas. You can have one base on each area. When you do your income shoots up from that area. At the moment i have 3 bases, and my main base appears to be the only one i can build labs and workshops at. The new bases can have hangars and detection systems etc.
The only experience with a base being invaded i had was when i was passing time at the 1 day mark, just to looka t the tech tree and i was avoiding combat, yes bases can be invaded, and you can build defences into any bases. So far i ahve seen laser defences, missile, plasma, and chemical defence. Only the soldiers situated at the base invaded can defend it. Although you can transfer troops via your carrier. Sadly as i was just passing time researching my troops died defending the base, so am not sure what happens afterwards. I have noticed that if you use a medikit or stimpack on injured troops their time spent in the hospital is much less, i have seen up to 30-40 days for someone who was incapacitated, and as littel as 3 days for someone you heal in the field.
As for shooting down UFO's. Yes you can use as many CAF's as you like, you start with 2, and i highly recommend using both, as your tech level is pretty poor, and even fighters can take your planes down 1v1. You can upgrade weapons shields, speed and capacity on all ships, and after a few upgrades you can send only 1 CAF to down the UFO's.
You dont manually refuel or or-arm the ships but after a fight you can see your money going down as they auto re-arm and fuel etc. And yes, if you fighting a UFO and another one happens to pass they join the fight, although im not sure thats AI, just unlucky another one passed by. Yes cash seems very hard to comeby unless your getting "Excellent" monthly reports each month you may struggle. If you shoot something down over water it is lost, so best to wait until they are above land.
UFO's seems to be different sizes, fighters look different to scouts, and the one cruiser i shot down was pretty huge, and jamm packed with aliens, i failed that mission. As yet i have no noticed any UFO damage on the tactical map that i remember, but i didnt really take note.
Maps seem randomly generated, although i haven't replayed enough areas to confirm. Aliens also seem randomly generated. Sometimes you leave your ship to see 4 shooting at you, sometimes most are still in the UFO. (im now used to lobbying a chem grenade or stun grenade out of the CAF's before sending the ground troops in, much safer) Hunting down the last alien is still a pain.
Yes you can sell, hopefully this screenie shows more than words. You can sell alien loot off, but its not worth much until you research it, then its price seems to triple. You can sell what you manufacture, however im no idea if it costs more to make it than you recieve for selling it as yet, didnt take much note of it.
Sorry the pic is a bit big, im not a techie, and unsure how to make it a little smaller.