If I have a normal TrueCrypt volume, and I want to create a Hidden volume inside of it, how do I stop the 2 from overriding each other? Or do I just have to manually make sure the inner volume does not go over the threshold?
There is a mechanism to protect the hidden volume when opening the normal volume it shares. It is described in the TrueCrypt documentation: http://www.truecrypt.org/docs/?s=hidden-volume-protection
When mounting the outer volume, Truecrypt has absolutely no idea that there is a hidden volume. That's by design. So you need to ensure that nothing writes to the outer volume when it's mounted normally.
Hidden volume protection is what you need when mounting the outer volume. Click mount options, then select "Protect hidden volume against damage caused by writing to outer volume" and enter the password for the hidden volume. Make sure the volume says "Outer" under type when it is mounted.
With this feature enabled, Truecrypt knows what area of the volume is taken up by the hidden section, and will switch the volume to read only if anything tries to write there.
When mounting the hidden volume, Truecrypt knows you are mounting a hidden volume and is only making the hidden portion accessible, so there is no risk of damaging the outer volume.
If an attacker forced you to mount the Truecrypt volume, you would mount the outer volume normally, without specifying the hidden volume's password. If the attacker writes to the volume, they may destroy the hidden volume, but will have no way to prove that the hidden volume exists. It is designed under the principle that you would rather have the data destroyed than in the hands of the attacker.