I know they both compliment each other but I'm trying to figure exactly how they both work together. Is it used for the anonymity? Sorry for the newb question, I have just really been trying to figure out the relationship these two technologies have with each other.
Monero will use I2P to connect nodes together. The goal of this is twofold:
an adversary spying on your network connection, like so many today, will not be able to see whether you are using Monero or not.
A node receiving a relayed transaction will not be able to tell the IP it came from.
A new I2P router, Kovri (https://github.com/monero-project/kovri/) is being developed for integration with Monero. The canonical I2P router depends on a Java VM, which is not ideal for weaker hardware.
Kovri will be usable by other clients than Monero too. Similarly, Monero will optionally be able to connect via clearnet (either only, or in parallel with I2). This is still a longer term feature.