Should work fine together but I'd consider a different HDD if you intend to use it as your boot drive, or get a cheap SSD.
I'd also consider swapping out the graphics card as it's a bit dated and you can get a 2gb faster card in that price range these days, the 2gb will help if you are using high res textures etc in Skyrim. HD7850 should be in your budget and Xfire capable. GTX660 is a bit more expensive but worth considering.
Nothing really needs PCIe 3.0 right now, and cards will work fine in 2.0, it's really just a future-proofing option.
If your budget is $800 to spend right now I reckon you can squeeze in an SSD and a better graphics card.
CPU+motherboard+ram+powersupply+HDD+case is a little over $500. http://pcpartpicker.com/p/nevF
If you are just wanting to get the best you can, that's a pretty nice budget for graphics.
All of those are potentially in your budget and all are a good amount better than GTX560Ti.
Alternatively, with a healthy budget like that you could go for a better CPU (i5 etc)
You really have a good amount of options.
Okay. So I've looked at the 7850 benchmarks and it's the graphics card I'll go with. (I'm only planning on spending $200 on the graphics card, so I can still afford it) also, if you can, post the newegg link for the hard drive (if it's on there) also, I think intel processors are a rip-off ($100 more for the same processor specs)
@ Graphics cards, 7850 is a nice card, very nearly bought one myself. If you are definitely intending on Xfire at some point you should make sure you are ok with microstutter though, AMD cards tend to be worse.
@ Processors. It's your call and AMD definitely have nice value, but any 2nd/3rd gen i5 is much better for gaming (and in general really). Whether or not it's worth the price gap is up to the individual. Friend of mine spent his entire "new pc" fund on a graphics card (~$450-500) and with a 4year old processor he gets near identical performance to me when I made a whole new machine (Ivy bridge I5 etc) because graphics are king.