Yes. Create "1" partition and then the other options should be available such as format which you need to do to format it as "Mac OS Extended (Journaled)". Once you've done that then you can continue to install OS X.
You'll never have the exact amount of what your HDD is, that 989 MB is correct.
awesome. so I guess I did everything right. Thanks! I really was paranoid. now I am running updates. The drive says its capacity is 999GB and free space is 989GB. wonderful!