On the question of whether to buy minerals from civ mines or not I would advise to always buy if you can afford it. There is a limited amount of everything in any one system and if the civilians mine it and you don't buy it then its gone. If money is tight then there is a order of precedence for which to buy and is based on how you pay for it so I will explain the system below.
Each civ mine is equal to 10 auto mines and for each civ mine you pay a set amount(250) for the yearly production. This means if there is only one mineral type where they setup then the yearly output will be only the annual output for that mineral. What this ends up meaning is that between a civ mine with one mineral and a civ mine with two minerals you will be getting double the minerals from the second. Now this is of course modified by the availability so if the first one with one mineral was at 1 and the second with two was .5 each they would provide equal total tons for the price. Luckily this all can be easily wrapped up by noting that the Mining/Maintenance screen for the colony will show you the annual production for each mineral individually and then as a total at the bottom. A quick example below from my LP:
Both Halleys Comet and Schaumasse has 3 civ mines. You can see that the Annual Production for Corbomite is the same for both yet the Total overall is higher for Halleys Comet because of having more minerals which overall are at a higher availability. This means that I get 3860 tons of minerals from Halleys for 750 while I only get 2154 tons for the same with Schaumasse.
What it means is that if have no specific mineral that you need then cut the mines with the lowest Annual output divided by the number of civ mines. Now of course you generally are needing some mineral or other. In which case you cut off the places without said mineral first and if you run out of those start cutting off those with your mineral at the lowest availability.
Also your mining rate tech affects their output so getting that up will let you get more bang for your buck. A somewhat interesting thing about the civ mines is that they don't seem to show up until you get your first populated colony as thats when the civs put out their first ships. This means if you delay setting up your first extraTerra population until you have a good mining tech you can get more bang for you buck overall and unless you where running a deficit you will have more money to spend as well.
This means the following order of precedence should be used for optimal mineral buying though of course it is always better to buy all the minerals you can. Also this is just a rough guide so if you suddenly realize you ran out of fuel and need all the sorium just go and buy it from all the mines with it.
1. Buy from Civ mines with the highest availability for the minerals you need
2. From Civ mines with the highest annual income overall divided by the number of Civ mines
3. Civ mines with minerals you have the least amount of with the highest availability
4. Any Sorium unless you have a supply of it and have already setup harvesters on a gas giant or two
5. Duranium, most everything uses it
6. Lastly is just whatever you will be using, if you don't use ground units you probably don't need to buy the mineral for it