Danger Will Robinson! Danger!
Do NOT buy an HP/Compaq system or you WILL regret it.
Long story short: HP/Compaq systems have very poor quality hardware, Windows gets very pissy on poor quality hardware, leading to you having a very poor experience.
Also, another little tip... Pretty much everything Best Buy's Geek Squad (and similar services offered by other stores) is completely useless, overpriced, and a lot of the people working there have about as much clue what they're doing as you do.
Case in point, the person you were talking to is full of it, or at best, highly confused. Here's a bit about how Intel, and AMD, make CPUs. Every single one of them starts off as a quad core chip, that is how they are fabricated. Now, some of those are going to have defects. Maybe one or two of the cores don't work properly, or even at all. Those chips are then sold as Core 2 Duos. In cases where three cores fail testing, they are sold as Core 2 Solos. Sometimes, if they need to ramp up production of a particular type, because there's a sudden spike in demand for Core 2 Duo chips, they may intentionally disable 2 of the 4 cores on a quad core chip, slap the Core 2 Duo logo on there, and ship it out.
AMD does exactly the same thing, except that they decided they would sell chips where 3 of the 4 cores were fully functional, which is probably very economical for them.
While it may be possible, using bits of trickery, to enable those additional cores, you have no way of telling if they were disabled because they didn't work properly or if Intel just needed to meet a demand for dual core chips and crippled some quad core chips to do so.
However, if you buy a system with a quad core chip, all 4 cores WILL be enabled when it ships. What that person at Best Buy is doing is quite probably illegal, but the majority of the things Geek Squad like outfits do is borderline illegal, and almost always highly unethical. Selling people services they don't need, pushing useless software and extended warranties, etc. Generally employees at places like Best Buy have a quota of things they have to sell every month, and if they don't do it, they're fired.
A little tip that most of us have learned through experience. Don't buy anything over $100 from Best Buy unless you need something immediately. Case in point, I recently moved half-way across the country, and thanks to some serious manhandling by UPS, my old computer died. I needed a replacement as soon as possible, so I reluctantly bought something at Best Buy. Only buy things from Best Buy when it's more important to have it right away than save 5-10% off the top. Or, when the hassle of returning something far exceeds any monetary savings. Big screen TVs come to mind for that one, or appliances like washing machines.
When it comes to computers, unless yours died and you need another post-haste it's probably better to buy direct. Also, decline all the extra services and software they'll try and push on you. The extended warranty is about the only thing I would consider, but you need to make a decision about whether YOU think it's worth the money.
I will say however, that for the most part I am pretty happy with this Dell system I picked up from Best Buy. Somewhere I swear it says the memory is dual channel, which isn't true, but dual channel memory really doesn't offer much of a performance benefit anyway. The problem isn't getting data from RAM to your CPU, it's getting data from anywhere else to RAM. It also comes with Vista x64, which admittedly doesn't enjoy the same driver support as the 32-bit Vista, but it's not really as bad as some people make it out to be.
Just do NOT, under any circumstances, get an HP or Compaq system. I don't care if it's from a store like Best Buy or direct from HP, DON'T DO IT!