I'm in the same situation, and I rarely post since Apple products are pretty intuitive to operate. I'm a Windows guy that has accumulated a Mac Mini, Macbook Air, 3 iPhones, and 4 iPods. Let's just say I've given them a bunch of business and recommended Apple to others.
The problem I see is that while they have a nice GUI, they have a very confusing infrastructure, and I started running into the multiple account issues prett early, and it was only for a few songs. I think that an early warning to the effect that "you already have an account that is billed to your current customer profile" would have prevented this mess.
The real problem seems to have started somewhere between mobile me, and the cloud service. Let me say up front that my original iTunes account was not an email account and contained no @ sign or .com. Since there were many Apple infrastructure changes this year, I remember being prompted for an email address rather than an a simple account name.
It seems like when two lives merge, as in a marriage, the accounts should also be able to merge. In addition, when both accounts trace back to a single individual at a single street address, this should not boil down to someone suggesting that "the agreement is clearly defined here" but the ability of someone at an Apple store to or LIVE customer service to say, let me help you with that, but we may have to wait a month until our engineers solve OUR problem.
I may sound like the typical "nothing is my fault" consumer, but I feel that there are two things that set Apple apart from it's competition. One is just great product design and interface control, and the other is superior customer support. If the customer support piece slips, I think Apple risks losing a substantial part of it's advantage.
I am trying to live with the effects of having these two accounts, and any solution must enable me to pay only once for the music, applications, etc. that I have purchased from Apple. For Apple to continue with things like cloud based strategies, they must remember that the consumer experience does not stop at the device itself, but continues through Apple's support systems and infrastructure.