The upgrade chips work relative to the type of weapon engine selected, and particular engines and tips are selective about what types of upgrades they'll best support. For instance, upgrading Damage on a Pulse Rifle (Military Engine + Repeater Tip) gives you a very poor return on investment, even with all chip sockets occupied, while upgrading Damage on a Contact Beam (Plasma Core + Precision Tip) increases the weapon's energy output greatly. Likewise, increasing clip size on the Pulse Rifle will give great increases in ammo capacity, up to twenty or so additional rounds, while upgrading the clip size on the Contact Beam gives negligible increases, at most garnering an additional couple of shots.
The values that are applied appear to be additive, instead of multiplicative. You'll receive the same increase in quality for each chip added from a particular category. As was indicated by the previous poster, certain values are applied to both tools at the same time, particularly the Reload stat. This is because when Isaac reloads the weapon, he reloads both tools simultaneously, so the weapon's reload time is determined by the slowest-reloading tool. By adding Reload chips to both tools, you can make a slow-loading gun, like the Rocket Launcher (Survey Charge + Directed Suspension Field) into a particularly fast one.
Ultimately, the number of "tick" increases that chips contribute to in the stat bars are arbitrary, based on the weapon, because of the bias each weapon has for its best upgrades. Upgrading clip size on a Rocket Launcher adds less than a quarter of a tick with each +2 circuit added to it, making it a very poor stat to upgrade.
Best thing to do is to experiment with engines that complement each other's reload times to get that out of the way, and then focus your chips on one particular skill that each gun excels at. Pulse Rifles are about fire rate, Contact Beams are about damage, etc. Only a few guns, like the Plasma Cutter, allow you to nearly max all their stat bars, so don't get too picky about it.