The winches on the cockpit coaming are called sheet winches, it looks like you have one set, which would make them your primary sheet winches. The winches on the cabin top are for most anything other than jib sheets.
My C&C 30 recollection is that the primary winches are positioned so the jib sheets can lead directly from the jib blocks (aka cars) on the genoa track to the primary sheet winch, and operate properly. MY boat had secondary sheet winches, so the primaries were further forward on the coaming. Hopefully your genoa tracks are long enough that you can lead the sheets for all jibs (150-130-110-90 or whatever sails you have) through the re-positioned cars. If you need to use blocks on the toerail for any sails, you'll lose about 10 degrees of pointing.
The only thing that should affect how the sheets trim is whether they are coming onto the winch at the correct angle, so they do not bind or override. See "angle" in here: http://www.harken.com/pdf/48.2_05.pdf
. If the sheets are not coming at the correct angle, you need to put the winch on pads, or add turning blocks, but your C&C 30 may not need such changes. If the angle(s) to your primaries location is a problem, so with turning blocks, as a turning block ensures the proper lead regardless of car/block location.
A picture of the sheets under load would help identify what is wrong.