Whenever I update a piece of code, I would like the version be reflected in pkgver also, so AUR tools like yaourt can inform the user. Any suggestion ?
Simply put, you can't do this. PKGBUILDs uploaded to the AUR are immutable. Nothing is going to magically change the pkgver short of you uploading a new PKGBUILD.
Well, you can do it. Manually. Everytime there is a new commit in the upstream, bump the pkgrel and upload to AUR. Users who call `yaourt -Syu --aur` will get an update. That's the only way.