At the end of each month, any facility, ship, researcher or technician of any base cost you money (maintenance, salaries). With many bases, researchers and/or technicians, the costs may exceed the income, particularly if you also want to buy things the following month.
The following "cheat" (well, technically, it's an exploit of a design flaw) can help:
The key fact is, any ... of any base; yet things in transit (transferring between bases) aren't counted toward a base, so they cost nothing at all.
At least two bases with unused living quarters and a base with an unused sub-pen.
What to do:
At the last day of the month, late enough that a transit would complete the next day, reduce research and manufacturing to 1 person (to not loose current progress).
Transfer all personal from base A to base B (where ever free room is) and personal from base B to another base (can be A if A has free room). This will basically swap the personal completely. Can also be done with the aquanauts.
The same procedure can be done with Baracudas and Tritons (and the later ships) as well, simply transfer from one base to the base with the free slot and so on.
End of the month:
You payed a few hundred thousands for the transit and saved millions to actually pay (for) them/it.
Once the transit is complete, send the personal back home and let them continue working like nothing happened.
If you transfer your Triton and those aquanauts, you also save money, but you risk to be unable to send your team to vital missions (terror sites or artifact sites), which may happen directly at the beginning of the new month.