You absolutely can put it on the lower lashes, but just by blinking, you get enough of the liquid on there for the effects to occur. Thus, separately placing it onto the lower lashes is wasteful.
Actually, you can put Latisse on the lower eyelashes but it is usually not necessary as some of the Latisse that you put on the upper eyelashes will migrate to the lower lashes when you blink or close your eyes. If you don't see much improvement in the lower lashes after a few months you can try applying Latisse there as well. By the way, Latisse was also shown to be effective in the treatment of eyebrow hairs in the January, 2012 issue of the Journal of Drugs in Dermatology.