Yay, SMAC! I miss it, having been deprived of real civ for so long. Wish I didn't lose my HD.
1 ) Manual terraforming is definitely the way to go. While auto-terraform is generally smarter than it is in Civ5/BE and has more options, manual terraforming is useful for turn advantage.
Forest planting is preferred on higher difficulties due to the low cap on content citizens, but farms+solar collectors work okay. Forests have advantages and disadvantages, the worst being that hostile infantry in your territory gain a defensive bonus... unless you have psi units.
Forests have a flat yield of 1/2/1 on non-bonus tiles, while a tile's productivity is normally based on raininess and rockiness. Additionally, without a bonus resource, tiles are limited to 2 food/2 nut/2 energy, so farms on rainy tiles don't perform as well as on would hope.
Generally, if I'm on high-altitude moist (over 1000m) or any altitude rainy, I'll go with solar collectors and farms, even though Forests are the "right" way to play for a lot of reasons. Arid has to go with Forests unless it is at a high altitude.
Later on there are more options, both for forests and other terraforming improvements like Boreholes and Condensers. The in-game encyclopedia is a fairly reliable resource for information on those enhancements when they are available. The Forests option reduces eco-damage and has strong production by mid-game, but once you have hab complexes and drone control, you will want bigger bases with or without crawlers.
2 )Yellow civvies are content, blue are "happy", red are "unhappy", and there are specialists are considered content (not sure if drones can be used for specialists, I think they can though). Specialists are normally there to offset temporary drone issues with Doctors, but can also be set to Librarians for science. There are improved specialist types later in the tree, with Empaths being the earliest for most tech paths.
Anyway if you have more red civvies than blue, your cities will revolt (no production/tech/income). Yellow don't count for either.
If you have no red and more blue than yellow, the city enters a golden age which confers some useful bonuses. This only happens with luxury spending.
Most drone control buildings will only prevent red civvies from appearing, and you would prefer not to have any red drones. Same with military police.
You will get red civvies from having too much population in a base, having lots of bases (where drones will randomly pop up), conquering a base (the occupied base will have extra drones), and having military units out of your territory while operating a free market economy. The latter of these is the most devastating, because drones from military units can not be negated by anti-drone buildings.
There are some alternatives to drone control / luxuries for dealing with drone riots. One is nightmare fuel and not a good idea, and another comes early-mid game and has similar penalties (except one is an atrocity and the other somehow isn't? Planet logic...) Late-game there is a wonder which suppresses drone riots outright with none of the negative effects.
3 )Cities get free energy based on your Economy rating in Social Engineering, and buildings. By default I think bases get 1 energy, +1 Economy gets +1 energy per base and +2 Economy gets +1 energy per tile worked. Higher Econ ratings give more energy per base, while negative economy ratings remove the free energy per base at -2, and remove the HQ's extra energy at -1.
If you are playing a faction capable of it, look up pop-booming to set up your early game economy - Democratic, Planned and a Childrens' Creche (or a Golden age in place of any of those, but that is expensive and stalls once you start getting drones; also Eudaimonia but that is way too late in the game). +6 growth puts your cities in population boom and they'll grow every turn. So long as you have drone control ability and food, this will swell your population to levels where you can really accelerate your game, and the AI doesn't do this often due to their SE preferences.