I'm guessing that you let iTunes automatically sync your iPads for you, you could have more control if you turn this feature off but you can still customize the content on each device even if you auto sync. Here's how to do it.
The first thing to do if you don't want every app to download to both devices is to go to Settings>Store>Automatic Downloads and turn them off - apps, music and books. This will prevent your iPads from downloading each others apps, music and books on it's own.
When you connect your iPad to iTunes let it go ahead and sync. After it syncs, do not disconnect it yet. Right click on your iPad's name on the left side of the iTunes window - under the devices heading and select transfer purchases. Then go into each tab in iTunes - at the top of the main window on the right - Music, Apps, Info, Movies, etc, and select the items that you want to put on your iPad - or deselect the items that you want to remove from your iPad. After you have gone through all of this sections, click on Apply in the lower right corner of the window and the changes will be made to your iPad's content. You have to make sure that you also select the main headings in each area of iTunes as well - put a checkmark in the box next to Sync Music, Sync Apps and so on.
After you disconnect your iPad, connect the other iPad and repeat this process. From this point on, iTunes will remember each device and when you sync your iPad, you will not end up with the content that you don't want on it - only the content that you selected for your own device.
You can experiment with this and you have nothing at all to lose if you make a mistake since all of the combined content will still be in your iTunes library on the computer and you can always sync again to replace or remove content.
You can share content with as many iDevices as you like, there is no limit - even if you own one hundred iPads - As long as you use the same Apple ID and account to download and purchase the content.