I came across a similiar situation when I bought my iPad 3 while still retaining my iPad 1 which my wife uses, though I did manage to work out what I needed to do... Apologies in advance if you find below I'm stating the obvious... but the following may be useful too for users who have never used iTunes.
Quiet simply you can share your downloads with any other Apple device you own as long as you only have one Apple Store (iTunes) account... meaning there will only be one main iTunes library on your PC.
When you connect your device to iTunes it knows which device it is, but you need to click on the actual device name (halfway down on the left) to select what items you are installing, or to see what's installed on that particular iPad ect..
The device name only pops up when a particular iPad device ect is connected, you can rename the devices to something more meaningful.. Like iPAD ONE and say iPAD THREE, which is what I did.
Think of your main library as being a central source where every app or download you buy will be stored..including those you drop in iTunes yourself.
This main library is always visible to ALL devices by clicking the Library options on top left, regardless of which device is connected.
However, if you click the actual 'device name', it then shows the various apps,music, videos, ect, thats currently on that device... including the layout.. you can also move apps into a particular order if you wish, and it will be replicated on your device. You also have the option to select 'ALL' or individual apps,music,video, books etc which you want put on that particular device by ticking the varous tick boxes. iTunes remembers these settings for each and every device you connect.
It got me a bit baffled at first until the penny dropped.. I may not have explained too well.. or I may have misunderstood.. but basically the above is how iTunes works.
If you had 2 totally different accounts, you would need 2 totally different libraries on your PC taking up a lot of space, and the big negative is you would have to pay twice for the same apps...so a not good idea.
Just think of the main library as being a central pool for all your iTunes software from which, each device can individually select what it wants, simply by clicking on the 'DEVICE' name, which pops up when the device is connected on the left side.
Hope I've managed to explain sufficiently for you to understand.. though I may have mis-understood.. won't be first time.
On a personal note..I prefer that iTunes does not automatically sync until I tell it to.. I just find it better that way.. but that's just me.