Shopify apps are awesome, and a major reason the Shopify platform is so successful.
Instead of employing a bloated interface, packed with add-ons you'd never use, Shopify provide a lean, robust store system where you simply add the components you need, nothing else.
Shopify apps are complicated, and are developed by experts in their respective fields. It is an app developer's responsibility to support their own code and to help customers install into themes, no matter who the themes are made by.
There are hundreds of apps, outnumbering themes 8-1, and many apps require updating on a regular basis; it would be impossible for us to test all apps work with our themes, as updates are frequent and not publicised.
We do not offer free support for third party code or apps. We also do not test that apps work with our themes, it is the app developer's responsibility to help install their application and code into a theme.
If an app breaks or affects the way your theme works, your first point of contact is the app developer - they should be able to help you get things working, and they are always welcome to contact us directly if they have questions about our theme code.
If you struggle to get help from the app developer, we have a developer team for hire at $120USD per hour (£90 +vat in UK). Please contact us if you need to hire us: shopify [at] cleanthemes.co.uk
Have fun with apps, many of them save lots of store management time, and many really help conversions; remember to not add apps 'because you can'! Grab the apps you need, and keep your store lean and productive :)