They control the number of times the two CPUs get to execute independently. Normally it's 1:1, but yoyo apparently found that giving each more time would run faster than the 1:1 ratio. It was one of his ways to solve the performance problems with the formats.
For example, in the case of Dreamcast if you have it set to 5, it lets the ARM7 execute 5 times in a row, followed by the AICA mixer 5 times in a row. I don't quite understand why it helps, but it does.
In some cases, this messes with the timing of the music being played, which is why I submitted my changes for 22khz playback instead. At 22khz, the iPhone 4 can handle most DSF files just fine with the correct CPU ratios of 1:1.
in fact there was a small issue in v1.6 with your patch: the arm cycles executed was divided by 2, leading to slowdowns in some songs. it is fixed in current dev version (github) but for sure it will impact performances...