You should have a site builder role that is distinct from the module developers and themers on your project. The site builder is the person in charge of the site, not the coders! A typical professional site has several content creators, several module developers, a themer, and several project managers of various types. Avoid the temptation to mix the roles. Installing, updating, and configuring modules and themes is easy to do if they're properly designed and documented, but they rarely are. Make sure they are, by separating responsibilities – don't let the module and theme developers install and turn on their own modules and themes, make them turn them over to the site builder, who has the time and incentive to keep track of (and document) how things fit together -- and who can extract the necessary information out of the coders, if necessary.