You can set the Style at any time, the simples way is to use the Global NPR tab in the Styles palette.
All you need to do is to click on any of the style and it will be applied globally to the whole document.
Apply Style on a Per-Object Basis
You can apply NPR style only to a certain objects. This could be done by using the NPR Settings that can be accessed by clicking on the Global NPR Style button on toolbar or using menu Project - Global NPR Style.
The settings will be examined in another topic, but to apply any preset or custom settings to an object or selection of objects use the Apply to Selected button on the Global NPR Styles.
Apply Style to Packages
Each package can have its own Global NPR Style, but if you want to apply a single Style to all objects inside packages use the Process Packages (Recursive) option on the Global NPR Styles.
Otherwise you can switch it off, then open a package and set a completely different NPR Style as a Global Style Inside Package, then close the package. This way you can easily mix various styles on one document and keep it all clean using packages.