For instructions on creating the basic custom UI solution, see Creating a Custom UI Solution for SharePoint.
With the masterpages done and other elements in order as well, it is time to deploy the solution. The solution contains a feature, and the activation of this feature will add the MasterPages and possible PageLayouts in the MasterPage Gallery of the SiteCollection, but unless we have a feature receiver to go with the feature, the rest is manual work.
To better understand the different MasterPages and their behavior on different types of sites, see About SharePoint 2010 MasterPages.
The first step for MasterPage automatization is to create a feature receiver that sets the MasterPages for the sites when feature is activated. Note, that if the feature is scoped as Web, it needs to be activated on each site separately. If it is scoped as Site, it is activated only once for the Site Collection and sets only the MasterPages of existing sites.
Add a feature receiver to the feature by right-clicking the feature > Add Event Receiver. Uncomment the FeatureActivated and FeatureDeactivated methods. For the FeatureActivated, insert the following code:
Note, that the MasterUrl sets the System Master and the CustomMasterUrl sets the Site Master. Foundation sites do not use the CustomMasterUrl at all, but it doesn't matter that it is set on those sites too.
For the deactivation method, copy-paste the same code, but change the MasterPages to e.g. v4.master and nightandday.master.
If we want to take this one step further, we can do some site identifying and set different MasterPages for different sites by their ID. E.g. the search site needs its own MasterPage, so we could add some code to the feature receiver so that it sets the search sites to use the custom search master, or if there is none, to keep using the default minimal.master:
You can check other site IDs e.g. in this article: Know the site template used for the SharePoint site.
Update your deactivation method likewise.
The feature receiver takes us as far as taking care of the existing sites. Next, let's take care of the new ones. Add an Event Receiver in your project:
Select Web Events, A site was provisioned:
Replace the default content of the method by the following code:
If you didn't use any ID-specific MasterPage settings in the feature receiver, you can disregard the if-else here too.