Installation of features and modules settings can happen automatically by creating a .config file for installation and then visit the /Setup/Default.aspx page.
For external features you should create a folder in your UI project at /Setup/applications/yourappname/FeatureDefinitions
and put the config file there for installation. Then during post build event you copy the whole folder /Setup/applications it up to the main Web project. You see example of this in WebStore.UI, it has a folder /Setup/applications/webstore/FeatureDefinitions and this folder has a text file in it named 000_WebStore.config
This file will be used by the Setup/Default.aspx page to install the feature and install module settings.
You need to create a new Guid for your new feature and use it for featureGuid in this config file. You can generate a Guid from Query analyzer using SELECT newid() or in .NET code with Guid.NewGuid.ToString()
There is some documentation here, but not very extensive.
Hope it helps,