Guitarist,
I face a similar situation... I have the following:
A. My primary account with Apple aka Apple ID #1.
Due to Apple @#$%&'ing my ID, all of my Apple related purchases and services via the Online Store, Mac App Store and iTunes Music/Video/App/etc store, and such are affiliated with a secondary email address now and connected to Apple ID #1. Think of it as my entire history with Apple. As a result, I also have an iCloud account affiliated with this ID.
B. The "new" account with Apple created due to their error. Call this Apple ID #2.
This is a completely fresh account with Apple. No history. No nothing. This account has an iCloud account affiliated with it. Due to Apple @#$%&'ing my Apple ID, this account is connected to my primary email address.
C. A MobileMe account. While affiliated with an Apple service, it is not an actual Apple ID.
While I have this account, the sole purpose I signed up with MobileMe was for syncing contacts between my IPhone, home computer, my office laptop and office desktop. I took advantage of a few other benefits such as online storage and MobileMe gallery, I can do without them easily. The syncing of my contacts is very important and handy.
My plan:
1. Use Apple ID #1 has my "purchases" account with Apple. this ensure my long history with Apple as well as my purchases and such stay intact. I'll maintain access to everything and not have to "purchase" apps and such all over again. That this account is affiliated with a secondary email address won't have a bearing on the matter. Every once in a while I will sync this account with iCloud to ensure it has a reasonably current copy of all my contacts. (I will not be using iCloud for email and storage)
2. Use Apple ID #2 as my "iCloud" account.
I will use this account for syncing contacts between my home machine and my IPhone. At some point, I'll transition my office machine to OS 10.7.x and at that point, it will get synced via this account as well. I kind of like the idea of separating my "historical" Apple ID (aka Apple ID #1) from my iCloud configuration. Apple can be flakey when it comes to online services. So, in the event Apple discontinues iCloud, it will have no impact whatsoever on my primary Apple ID. Apple got rid of EWorld, ITools, and is in the process of discontinuing MobileMe. Who's to say how long Apple will maintain iCloud?
3. My MobileMe account will remain active until such a time Apple discontinues it entirely. That way, my IPhone and home machine will retain the ability to sync contacts with my office laptop and office desktop. Once Apple discontinues MobileMe, I'll find a different way to ensure the contacts on the hardware I own that isn't iCloud friendly. The easiest way will be to archive my contacts. Once I've archived the contacts, I can easily import them into Address Book on both my office laptop and desktop. A tad inconvenient but very doable.
On a different note, all of my friend and family use my primary email address for contacting me via email. Since FaceTime requires an Apple ID, I'll use the ID affiliated with my primary email address (Apple ID #2 - my iCloud ID) as my FaceTime ID. That way, if people want to video chat with me, they simply use the same email address for me they use for everything else.
Robert