About how many documents would you say these 40-60 users produce in a month? Actually, I should ask about size. Would you think you guys produce 500MB of documents in a month? 1GB? 10GB?
Depending on the amount of data you guys will produce, you probably won't need too many document libraries. The way we do it as a division, and has worked well so far, is that we have one top level library for files that need to be shared throughout the entire unit with everyone having privileges to share inside of. Then every section/sub-unit has their own site with their own document libraries in which only people in that section have privileges to.
With 60 users and the main focus being just document sharing/collaboration you can use one single site collection. This is good, as navigation and other features are harder to manage with multiple site collections. Plan the hierarchy of your sites out in advance though for sure. Think about how your security groups will be as well.
You might be able to get away with just an overall Site Owners, Members and Visitors group but you should generally have a set of those(or more) groups for every site.
As in IT Owners, IT Members, IT Visitors then for HR you have HR Owners, Members, Visitors and do the same for every other section. It might seem like overkill for only 50ish users, but it's a lot easier to manage and know exactly what someone in each group can access.
Leave all permissions as inherited until all your sites are created, then break the inheritance then. That way you can just remove privileges from a few sites, instead of adding privileges to a ton of sites.
If my thoughts seem all over the place, it's because they are. I'm just throwing tidbits of suggestions at you that I wish I had thought of or heard of before I began my first installation.
If you don't have an SOP yet, or don't do that in the civilian world, you should think about getting one in place before the site goes live. Have a proper naming convention for files in place before everyone starts throwing random **** called "document.doc" all over the place. Something along the lines of the name of the file, the name of the project it's related to, and the name of the section that produced it. Use underscores, not spaces. This is just a general rule of thumb for anything going on the web.
Also a part of the SOP, should be a 3 deep rule for document libraries. Basically, if Section A is hosting files and any other section is expected to see/use these files, then they should never be deeper than 3 folders inside that document library. Really important stuff, should be no more than 1 folder.
