Feeding the pickup to one of the analogue pins directly probably won't do as these pins aren't updated fast enough (causing glitches as the input goes over the nyquist of the input) and the precision is probably to low to detect the pickup-input differences.
If you want to use it as some sort of gate (selecting which string is being played), you'll need to use a full-wave rectifier, gain and a slew function to create a gate-signal, which could then be send to either an analogue or digital input.
I've been trying to make a polyphonic pitch detector, but with limited results and quite a high cpu-use (worked quite well with sines, but screwed up when input became 6 complex waves at once). But I think some sort of poly-pitch detector should be able to bring you where you want. Perhaps you do a limited poly-pitch-detect with a cross-over filter and then put a pitch-detector over each band.
You said you want to get the pitch of the lowest note being played.. which is of course different from reading multiple pitches.
If you use a LP-filter, set to quite a low frequency cutoff, it will force higher frequencies to always be of lower power then low frequencies. The pitch-detector will then always detect the lowest frequency as it's the biggest influence on the zero-crossing, thus giving you the bass-note. Though note, it depends on whether you are actually playing the key-note of the chord as lowest note.. you could also be playing a third, fourth or fifth as lowest note when playing an inverted chord..