Generally, I place G-C pairs on multi-loops with the G on the right as looking from inside the loop, i.e. on the clockwise side looking from the top. Per the strategy guides, I test where to put extra G’s on the loops to further reduce the energy. In my experience, placing the extra G’s on the counter-clockwise side of the G-C pairs - next to the C - usually lowers energy, but it never does on the clock-wise side.
Occasionally, adding G’s doesn’t change the energy. In those cases, I try adding C’s on the opposite side of the pair - next to the G. Sometimes this does reduce energy.
Is there any reason not to use C’s this way? The strategy guides I’ve read so far don’t mention this; they only talk about adding G’s.
Using the “G”, guanine is usually the strongest way to lower the energy in the loop but this isn’t a “hard and fast” rule that must be applied at all times. Players are first introduced to guanine and for the single state challenge puzzles this is all that is required to be used to solve them for boosting in loops. This is why it is first taught. However, as you progress, and as you are discovering, there are a number of other combinations.
I think you will enjoy reading the section on “Multiloops” from the guide, Tips and Tricks". I’ve enclosed it below.