I puchased Master collection CS6 and I have a cloud subscription. How many computers can I use and can I work on Cloud files from the computers that have the full purchased version installed?
To answer your last question, yes. You can create files from any Adobe product, upload them to the Creative Cloud, and then download them to another computer and work on them just fine. The Adobe applications you downloaded from Creative Cloud have the exact same functionality as a version from a box! The Creative Cloud is simply an online storage and file-sharing service that Adobe provides to subscribers.
With your Creative Cloud subscription you are allowed to download the applications on two computers (but you cannot run the applications at the same time). Similarly, you can only download your Master Collection on two computers. Therefore, if I understand your situation correctly, you can install your applications on a total of 4 computers.
I have a backup Mac (for emergencies) that has a copy of most of my software - should my main machine fail or throw a wobbly. I have a copy of some of the Adobe software on my laptop. InDesign on the laptop now says Maximum Activations Exceeded when trying to use out of the office. (This was not an issue originally). Do I need to remove the software from my backup Mac to solve the problem or is there something else I need to do ?
You can deactivate the software without having to uninstall the applications. Simply open InDesign on your backup Mac and in the Help menu choose Deactivate.
If you're getting that activation message, this would be the simplest test to troubleshoot. Of course, if you're 100% sure that you only installed the applications on two computers (your laptop + backup mac) then I'm not sure why you would recieve this message.
If it turns out that another computer does have the apps installed, you perform the same operation (Help > Deactivate) to resolve the issue.