New Construction
The equipment installation phase may take place in several stages. Some equipment more tolerant to dust can be installed while work is still in progress. Items like in-wall or in-ceiling speakers and some volume controls would fall into this grouping (although it's always best to completely cover items with plastic when possible).
Many in-wall speakers are designed to be painted to match the color of the surface they will be attached to. When possible, having speakers sprayed prior to installation will yield superior results. Speakers have perforated covers that will clog easily if care isn't taken during painting. Your painting contractor is the best person to speak with about this.
When the levels of dust caused by construction and finish work have subsided the main components can be installed. After installation, keypads, wall-mounted touchpanels and electronics will still need to be protected with a plastic covering of some type until the space is completely cleaned.
Retrofit
Equipment being installed into an existing home has very few of the limitations of new construction. As long as the required cables have been run and the space has been cleaned, the components can be installed and connections made.
Actual placement of the main components may all happen towards the end of the project. This allows for all of the connections between components to be run with less interference.