MAplot() uses ggplot2 to do the plotting, so it's not as direct to deal with as base graphics would be. You first need to capture the output.
p <- MAplot(genes(cuff_data),'LC','LT',logMode=T,pseudocount=1,smooth=F)
I think there is an iron clad law that all ggplot objects are named 'p', so consider yourself warned...
You then tell ggplot what else you want to do, thusly
p <- p + geom_point(aes(A, log2(M), colour = factor(ifelse(log2(M) < 2, 1,2))), size = 0.8) + geom_hline(yintercept = c(-2,2)) + theme(legend.position = "none") + scale_colour_manual(values = c("black","red"))
The geom_point business just adds the color specification, the geom_hline just adds the horizontal lines, theme just tells ggplot not to make a legend, and the scale_colour_manual sets the colors to black and red, instead of the defaults of salmon and aqua. See the ggplot help for more information.
Edit: I forgot - you won't get a plot until you type 'p' at the R prompt