Latency and click track

When I set the latency value in “Preferences”, will this latency be applied to a new click track?
I want to generate a new click track and then record a first guitar part, play back the guitar and the click track and then record the second guitar part.
I am using a M-AUDIO Mobile-Pre USB interface and WIndows XP SP3. I am using a condensor mike to record the classical guitar.

Latency compensation is only applied to recorded tracks. It does not need to be applied to generated tracks because there is no latency to be compensated for.
See here:

So how does that work then?? Do I set the latency to 0 and then generate the click track, and the set the latency to the correct value and then record the additonal tracks???

No, just set up the latency correction for recording (as described in the link).
Don’t worry about latency with generated sounds, there isn’t any and latency correction is not applied.

Thanks. I will give that a try.