Insomniaclown, your approach is a good way to record everything and mix it later for very precise control over the entire frequency range of the instrument. It is similar to to the approach used by pro guitarists (with budgets the size of some small governments) use when they use multiple amps in their live rigs and blend a clean one with a scooped high gain etc. etc.
They can push high harmonics out out of one amp, clean out of another, and low end out of a third, then have other amps with their own individual specialized processing. You are limited then only by your imagination and budget. In the end it all sums up into a single signature sound profile as the waves compete, cancel, complement, and blend.
In the end, you are probably using a complex audio chain to reduce the string vibration "fundementals" and accentuate other weaker frequencies to achieve the sound you are looking for. It's a good way to go for recording because it allows you to change the sound at will after the tracks are laid down and dial in precisely what you want.
Doing it in an organized way and being conscious of what you did to the sound will allow you to set up a simpler and more specialized signal chain to get the same (or nearly so) sound, perhaps from a single amp in your live rig. Keep experimenting! It's fun, and will only help your sound (recorded or live) if you let your ears and knowledge be your guides.
Stevil: an excellent read, I like the guy's writing style! It's in my bookmarks now, Thanks.