Help a newbie decide how to set up Server
Sorry, no, I haven't. Part of me isn't happy that I'm doing someone else's job for them and the other part of me got busy with other things. Plus it's not currently flooding. 
Adrian,
Previous posts have pointed you to some decent sources of info. You don't provide much info regarding what you are needing the map server for, so we can only speculate regarding your true needs. You mention you already have Server Workgroup but we don't know if someone at your company got talked into buying a license and now you need to figure out how to implement it or if it was purchased by someone prior to you with more knowledge and they left before implementation and you are assigned to pick up where that person left off but with less knowledge.
Depending on your needs, you may be able to just use ArcGIS Online and pay Esri to host your data. You could get rid of the Workgroup license cost and put it toward AGOL and hosting. You already mentioned Amazon Web Services, which could save you from managing the hardware but I don't know how your existing Workgroup license might be leveraged (does it just transfer?). Both of these scenarios could save you from the hassles of maintaining hardware. Your overall knowledge level, such as with relational databases, should also be taken into account. It's evident that you have a willingness to learn but do you have the time and resources to do so? And what are the expectations of your employer? Do they understand where you are on the knowledge arc for Server or do they believe that because you "know computers" you automatically know Server? I have co-workers who believe I am a Windows desktop support specialist simply because my desk was once in IT (my job has always been as a GIS Coordinator). I call it "abilities by association". 
You also mention needing some secure services, so maybe your data is sensitive enough that you don't want it hosted off-site. Someone mentioned that Portal (should you decide to host AGOL in-house) is recommended to be on a separate server. You say you work for a small company. Depending upon how beefy your server is and exactly how small your company is (i.e. how many users are expected to be hitting the server/Portal at one time) you may be just fine with both on the same box.
I think the book that was mentioned would give you a solid contextual knowledge of Server--enough to be able to ask the right questions of Esri reps or maybe a consultant hired to take your use case and recommend a setup or course of action. Rebecca's comment regarding an EDN subscription could make sense, but once you settle on a possible configuration, you may consider asking your Esri rep to provide a six month trial license (if you don't already have the necessary licenses) to test the viability of your decision. I'm not sure if Esri does that much anymore but it would be worth asking.
BTW, SDE is part of ArcGIS for Server Standard (Workgroup or Enterprise), so you just need to have a compatible relational database (yet another additional cost/license and possibly another server box).
