Updates no prob if you do it correcly (obviously checking for original executable must be modified), and executable replacement depends on the installation used. Installshield Wizard uses abnormal .cab files, when other uses Windows Installer with standart .cab and .msi data tables. Other picky installation requieres more experience to be cracked.
Keeping the original exe is not a bad idea, but not necesary.
Only in Operation FlashPoint were an original checking and was easy to remove that check that does not came from outside. It checks some data into the ORIGINAL installation. You only needs to modify such data and voilá.
Good luck!
TIP: If you want, in this
web page we teach people how to proceed with most common installers. In the other way, this page is in spanish, so you will need to translate.