If you definitely want changes to be effective for all applications you're running now and and at all times you can imagine, edit the existing files in
/etc/apache2/mods-available/, otherwise modularize as early as possible by separating into different files.
The latter case should almost always be the way to go as you'll figure out much later that you can reuse a configuration and write it in a shared file (one that is included in the main configuration or one that you include in multiple files) in most of the cases. That's what files are for.
If you stick to the default locations (
/etc/apache2/mods-available/ is one)
dpkg would warn you if changes would be overwritten, yet it's more comfortable to not be warned at all and leave package maintained things be package maintained things and your files your files.