Using Resource Packages like Bootstrap there seems to be some overlap with Sitefinity Themes.
Question: What is best practice here?
For example, if you're using Bootstrap and you apply a theme to it, but you want to customize some of the widget styling...
Question: Where's the best place to put this? In the theme or straight in the Bootstrap Resource Package folder?
To maintain upgradability I would assume that one shouldn't change any of the existing files in the Resource Package, but you can for example add additional layouts directly to the MVC > Layouts folder or GridSystem folder for additional Grid Layouts. You can also supposedly add additional Widget templates directly in this folder.
Question: Is this the only place to put your customizations? It seems very messy since when you upgrade you'll have to create a backup of the folder and then hope like hell one of your developers hasn't customized one of the original files when you copy a new version over it.