this is an old thread but let me explain some basic methods which can circumvent to overspend production.
first off messing with the civ wide sliders to accomodate a few planets will not work at all since your other planets will suffer from that.
one good solution is to go all-lab and have sliders at 0/0/100 at all times.
youre building your colonys up with focus from research and once this is complete or you have to focus more on military prod simply do so.
every turn go into the planetary list and chack if there are ships or improvements ready in 1 turn. check how much sp or mp will be lost. (a good idea is to design ships that have the cost in its name) if its too much set the focus away and buy the structure/ship usually by using the first lease (it is somehow often cheaper than the direct buy)
this way you are not going to loose any production points.
or you design different ships with different costs (higher qualitiy ships) and shuffle through them (thing like an added hitpoints or range are good for this as they take very little space, but be warned that these ships carry the threat with them to cost more maint)
for research use the general slider or, if you always enjoy going at 100% capacity, shift into social production as well.
however, if you have planets with no social queue at all that would also be wasted capacity (not cost) so you shoudl at least have 1% military slider so the base SP can carry over to your MP.
so a balanced approach could look like this:
1/49/50 initally when theres alot of social to do, and later on 50/0/50* with the last remaining developments of the high PQ planets from focus.
howver, it is actually more efficient to go all-lab or all-fac, although it needs some practice or setup (such as in all-fac you're lacking alot of techs and you have to rely heavy on techtrade or stealing otherwise you will only produce rubbish and in all-lab consider buying ships from the AI and upgradeing them (both techniques work best with a strong economic approach which you will use to mitigate its weaknesses)
* once your planets are fully developed you can also switch to 0/0/100 to research some tech and once this is done hop back to 100/0/0 this is actually more efficient as it is kinda pointless to try to build ships which will be outdated turns later.