e.g. you want enable some new feature in mplayer, you have to
1. add/change --enable- or --with- configure flag in the PKGBUILD.
2. try building
3. install missing dependencies, fix up the pkgbuild to include these dependencies
4. try building again
5. if there are missing dependencies, go back to 3, or fix the sources, in case of build error.
6. in case you get stuck - wait for someone else who'll do it, or give it up.
in case of gentoo, you have to change one environment variable, and that's pretty much it. changing it alters dependencies, and the package manager takes care of it.
most well-written ebuilds cover all possible build option combinations for their package. (mplayer ebuild probably covers 95% of configure combinations).
also ebuilds can require their dependencies to be built with certain features enabled or disabled. e.g. amarok2 requires that mysql is built with "embedded" feature. you just cannot do that in archlinux.
the problem with arch linux ABS is - PKGBUILDS are static scripts. sometimes changing them involves a lot of work. gentoo ebuilds are more flexible in this regard - you need to alter the USE variable to make them build software with different set of features.