We are building our support site for our mhealth platform end users on desk.com how do we organize the content?

As is my way, I have to answer tangentially: People hate reading documentation. Essentially no one will read the quick start guide, and those who do will have poor retention. This is not just a pithy quote, but driven by years of research into cognitive psychology. You cannot provide training around a complex (or bad) interface, and short training like onboarding guides have essentially no impact.

If your responsibility is only the support systems: Ask the users. Carefully. You can't run polls and focus groups as they are not accurate but you can run (or hire people to run) "card sorting exercises." These are participatory design tasks where representative end users can help you understand how they would organize, group and label the information. That makes it more likely for users to find the information they need.

Ideally, and if you have authority to mess with the design of the whole application, you don't even need help. No, really! I have designed complex applications (used millions of times a day) with NO help system. It can be done. For this domain, I would probably expect a help system, but one based more around digging into details, and presented in that way, instead of as help.

For the interface itself, the application should instead guide the user, and if possible (based on information already entered, what you gather over time if it is something using biometrics or synched to records, etc.) automatically create the needed widgets. Users are very, very poor at customizing, no matter what they say. To remain sticky, make it easy, and personalize for them.

I'd be happy to chat about this more based on your specific needs if you are comfortable sharing them with me.

The best way to learn about organizing the content would be to check out other Desk.com sites (see their customer page for examples). The knowledge base is two tiers (topics and articles) so it's somewhat limited but very simple to set up.

I'll recommend you take a look at HelpScout blog (https://www.helpscout.net/blog/knowledge-base-article/) and intercom blog (https://docs.intercom.io/). They're definitely the best resources to dive into this questions :)