As per my comment (and also the comment in the middle of the @Justin answer) facet_wrap
may be the way to go. It generates something like the image below. Obviously you'd need to play around with colours, legends and maybe the order of the factors, but you can see the general approach. Code follows image.
library(ggplot2)
library(reshape)
mydf <- data.frame(day = 1:10,
upper1 = runif(10, 10000, 20000),
upper2 = runif(10, 15000, 16000),
lower1 = runif(10, 1, 10),
lower2 = runif(10, 3, 8))
mydf.melt <- melt(mydf, id.var = 'day')
mydf.melt$grouping <- ifelse(mydf.melt$value >= 10000, "upper", "lower")
ggplot(mydf.melt, aes(x = day, y = value, group = variable)) +
geom_line() +
facet_wrap(~ grouping, ncol = 1, scales = "free_y")