In my game I think I've gone overboard and I've built mining stations in every planet in every system and my cashflow is always in the red.
Mining station construction costs and upkeep are paid for by the private sector. State cashflow is not directly affected by mining stations no matter how many you build.
I will add that having negative cashflow is not necessarily a problem, as long as you have enough bonus income that you have a positive net income or as long as you have enough cash on hand to continue doing whatever you want anyways. Planetary facilities (as in the ones in the Facilities tab in the Colonies window), space ports, research bases, resort bases, monitoring stations, starbases, warships, troop transports, and troops directly impact the state cashflow; if being in the red on that bothers you, then look into cutting expenses in one or more of those areas (e.g. use a smaller space port early on instead of the size 5000 monster with 40 construction yards and 30 docking bays and a thousand firepower in pulse blasters and seeking missiles). Another thing you can sometimes cut to reduce expenses is armor; maintenance costs are related to the total resource cost of a component, and plates of armor are some of the most resource-intensive components you can add to a ship. You never want an unarmored ship, but maybe you can replace ten of the plates on the ships with 15 or 20 plates with a shield generator or something like that.
Is there some specific criteria to use to build them for best use?
The best mines are those that provide multiple resources that you need, are close to where you need the resources, and have high total (and preferably also high individual) deposit quality. If you can get three strategic resources with only one mine, that's two construction missions your construction ship doesn't need to do to cover all the basics, which means you spend less time and fewer resources setting up your initial mining stations. If your freighters only have to jump across the system rather than across the sector, they can run a lot more cargo missions in a given period of time than they otherwise would have been able to, and you also need to wait less time for shipments to start arriving to clear or prevent work stoppages due to resource shortages or alleviate fuel crises (though if a fuel crisis gets bad enough, nearby mines don't really help; they're all out of gas or all backed up refueling empty ships, so freighters trying to bring in fuel have to look far afield to find fuel anyways). High total deposit quality means high overall resource output per mine.
Note that none of these are hard rules. A location with an 87% total deposit quality which all comes from a steel deposit may well be preferable to a location with a 174% total deposit quality of which only 14% comes from a steel deposit, as even though the 174% total quality location offers roughly twice the overall resource output it has only about a sixth the steel output, and steel is a strategic resource for which there is usually a relatively high demand. A 2% chromium deposit in the home system probably isn't worth bothering about unless there are other resources you want at the location or unless the only alternative chromium sources are ludicrously far away or similarly poor.
Some other rules of thumb include having at least one source of each strategic resource per active (or planned) major shipyard and building mines over just about any fuel source of any quality. For that last one, exercise your judgment; a fuel mine off in the middle of nowhere or in pirate-infested territory where you cannot protect it probably isn't going to do you any good, and another fuel mine when you already have ten or fifteen decent sources but only have one or two low-quality sources of many other strategic resources and could do with finding a few more luxuries probably isn't a very high priority.
< Message edited by Aeson -- 7/27/2016 6:49:20 AM >