The IP protocol has no concept of layers. It consists simply of packets. When people talk about layers (often layer 2 or layer 3) they are actually talking about how to stuff IP packets into some transport medium such as coax cables, fiber, WiFi, or Ethernet. We will hardly have to worry about those layers, since IPsec deals with IP packets, and not the physical medium of sending those packets.
If you connect from one machine to the other, you are sending and receiving packets. A connection is nothing more than two machines remembering the state of the packets sent and received. An IP packet consists of an IP header, and the IP body. The header contains information that ensures the packets are passed along until they reach their destination. The header also describes what kind of data is inside the packet. The body is the actual data, or the payload.
Each IP packet's header contains the source address, the IP address of the machine that created the packet (and later on perhaps expects an answer). It contains the destination IP address, the place where this packet is intended to go, and a protocol number. Most protocols also require a port number. The IP header has further space for a bunch of other options or flags that can be set.