Although the stylesheetswitcher is a very handy widget for on the fly changing of stylesheets I'm not sure if it'll help you in this case:
1. if you have 'static' microsites in your project I recommend just using an extra classname on the specific pagelayouts you use and just put it in the normal theme. If - multitenancy being a good example - the theming needs to change dynamically for the same pages, the widget is surely a good answer.
2. Note that you can't really copy paste non-mendix themes into Mendix. It doesn't work that way. Surely you'll have covered the buttons and the navigation menu. But Mendix really is a lot bigger than just the standard Bootstrap components. Basically you'll be putting a lot of code in that will never be used from that Bootstrap theme and you'll still miss the biggest part of your Mendix app in terms of theming effort. Best way forward would be to just take the bootstrap theme as inspiration / input and just create the theme in Mendix. it'll probably be faster than trying to import non-mendix themes and fixing everything that's wrong with them.
Sid, check out this widget on the Mendix App Store, that allows you to load custom themes on-the-fly in your app:
Looks promising.; I'll follow-up about how this worked for me. Thanks Eric!