Possibly-Relevant Background Info:

I've recently moved up from icky shared hosting to a glorious, Remote Desktop-administrated VPS server running Windows Server 2008 R2.

Even though I'm only 21 now and a computer science major, I've tried to play with every Windows Server release since '03, just to learn new things. What usually happens is inevitably I'll do something wrong and pretty much ruin the install. You're dealing with an amateur here :)

Through the past few months of working with my new server, I've mastered DNS, IIS, got Team Foundation Server running (yay!), and can install all of the other basics like SQL Server and Active Directory.

The Problem:

Now, these last few weeks I've been trying to install Exchange Server 2010 (SP1). To make a long story short, it took me several attempts, and I even had to get my server wiped just so I could start fresh since Exchange decided uninstalling properly was for sissies (cost me $20, bah).

Today, at long last, I got Exchange mostly working. There were two main problems left, however, that left me unsatisfied:

1. Exchange installed itself and all of its child sites into Default Web Site. I wanted to access Exchange via mail.domain.com, but instead everything was configured to domain.com. My limited server admin knowledge was not enough to configure IIS or Exchange to move itself over to the website I had set up for it, appropriately titled 'mail.domain.com', which I had bound to a dedicated IP address (I was told this was necessary, but he may have been wrong).
2. I have two SSL certificates: one for my main domain and one for my mail subdomain. For whatever reason, I had issues geting Exchange to use my mail certificate, even though I had assigned the proper roles in the MMC. I did, at one point, get it to work (or mostly work, anyways. Frankly, my memory of today is clouded by intense frustration). Additionally, I was confused which type of SSL certificate I should be using for Exchange. My SSL provider, GoDaddy, allows me to request a new certificate whenever, so I can use either the certificate request provided by IIS or the more complicated and specific request you can create with Exchange. Which type should I be using, the IIS or Exchange certificate? If I must use the Exchange certificate, will that 1) cause issues when I bind that certificate to my mail.domain.com subdomain or 2) is that an unnecessary step?
3. The SSL Certificate Strikes Back When I thought I had the proper SSL certificate assigned for those brief, sweet moments, Google Chrome reported the correct mail.domain.com certificate when browsing https://mail.domain.com. However, Outlook 2010 threw up an error when trying to configure my email account claiming that the certificate didn't match the domain of "mail.domain.com". Is this an issue that will be resolved by problem #2 or is it a separate one entirely?

Apologies for the massive wall of text, but I wanted to provide as much info as I possibly could. Exchange is the last thing I'd like installed on my server, and naturally it's turning out to be the hardest.

Thanks for any info at all. Even a point in a vague direction would be a huge help at this point.

Thanks! -Eric

P.S.: The reason I keep ruining my install is that when I attempt to uninstall Exchange, something invariably goes wrong. The last time the uninstaller complained that there was still a mailbox active and it couldn't proceed until I deleted it. ... The only mailbox left was the Administrator account, the built-in one I couldn't delete. So I attempted to manually uninstall it following several guides online only to now be stuck unable to launch the installer and have to get my system wiped AGAIN for the second time today ($40 down the drain, bah!). I do not understand at all why "uninstall" just can't mean "hey, you, delete everything and go away". There's not even a force uninstall option, only a "recover system" option that just fails to fix anything and makes it so I can't even use the GUI uninstaller. </rant>