Okay, I hope this helps, but what I am going to say might seem counter intuitive, but you should start by using personal sites and NOT a central portal.
Personal documents on personal sites. Simple......... Now someone is going to want to eventually share those documents…. If at least when the person leaves….... For that they are going to need a new site. A site specifically for the documents they want to share.
Ask them what is the project that the documents are for? Create a project site for that project and put the documents into separate document libraries for each part of the project (NOT FOLDERS) and then you are simply going to assign ownership to whomever requested the site and step back.
Structure new libraries for individual phases of the project. Show them how to create new libraries, talk to them and guide them, but forget the idea of ownership of the site and once the project is over then close write access to the site.
From here on forget the idea of a rigid structure and think of it as a dynamic disparate sites for specific projects, meetings, document types / sets, events and anything else. Forget the idea of customisation initially, if you are going to do web design and customisation up front and it is just you then you are definately doing it wrong and you're going to end up in a world of pain. SharePoint customisation is a nightmare and quite frankly isn't going to put you in happy land. Creating a nice site doesn't make for happy users of that site
You also don’t need to directly join sites under a hierarchy, in fact STAY AWAY from hierarchies all together. Information should not be stored under hierarchy. This is usually where people go wrong with SharePoint. It will cause you a lot of pain to use it this way because people will treat it like a file based system (because that is what they know) and it just is not like that.
So if someone wants visibility of other areas of work, projects, meetings and whatever else then they need to be given permission by the sites owners. They will receive an email with a link... If they want they can create a shortcut initially and if you want to show them how to add a link it into their personal site then all the better.
SharePoint has some strengths and weaknesses and where Microsoft has other products you are going to find its weaknesses. What SharePoint does well is integrate everything into organised places and this is the one thing you should be focusing on doing first. If you want to integrate ideas and content from separate sites then look into Yammer and News feeds as your content integration tool and by adding them into user portals. You should be joining pages through news feeds to target relevant information to the end user. But before all that just start by solving problems, providing project sites, team sites, sites for social events.
Just stay the heck away from any sites for individual teams and organisational units. Honestly say NO.
If managers want to do this then your organisation has problems because this is how you create silos. A example of this is where your boss hates the other teams boss because he is threatened by him or her or for whatever reason they dont want to share work outside of their own team... even though you work for the same organisation... you have the power to stop this and sell this idea to your stakeholders. It will make you look good.
Keep sites small and specific for particular topics. Think of them as disposable bubbles that once done with you LOCK and use purely for reference, heck even delete if no longer needed.
You should guide and watch how people use them and then create templates based on HOW they went about storing inside of them.
SharePoint is weird in that it provides out of the box areas that are initially kind of clunky, this is because they are meant to be developed and shaped, but initially it is okay for this to happen. Just explain that you are doing just that.
Start by practicing building sites for yourself, for this very project build a project site… JUST for this… nothing else..... speak to stakeholders and create meeting sites for them to document ideas and record information discussed… look into how you integrate them directly into Outlook (I think 2007 onward allows this), so when they create a meeting it automatically creates a site…. It will wow them in fact focus initially on just that… Any cool feature you find, create a demo for so you know how it works and so you can demo it and then use it.
Create working content to meet their requirements, demonstrate it working to EVERYONE, demonstrate it not working to everyone and get feedback. Find people who are interested and get them involved somehow... Just keep speaking to people and building new things for them... be iterative and helpful.
Some further points:
SharePoint is MASSIVE, a lot of people hate it, but it is just very difficult to get a grasp of stop thinking of it as central site with sub sites and use it as a platform to store information... I could go on, but you really need to learn to get to grips with it yourself. Also like any project and resource it is a good idea to find out who your stakeholders are and find out what they want.... Don't start developing until you have met with them and discussed what they would like to see because ultimately they are going to keep you rolling on wards.
Finally unless you have many 3rd party or in house applications built into SharePoint then I would also seriously consider moving to Office 365. The cloud is 100% where MS is moving and the benefits out way the risks to integration.
The massively difficult part of being in charge of document management is keeping people enthusiastic, keeping them in check and ultimately keeping involved. You will meet a lot of resistance, but be sure of yourself that they are wrong.. classic resistance to change... you are the expert.. Don't tell them how to do it, show them... show them the advantages and ultimately build stuff and demo stuff that makes their lives easier.
The key to success though is stakeholders stakeholders stakeholders .
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