Hello,
In the your setup, the Raspberry Pi is the I²C master, so it needs to communicate directly with the sensor chip; the AVR will not be involved. To be clear, you are using a Romi 32U4 Control Board, right? Unfortunately we do not have any complete example code for controlling the LSM6DS33 on that board with a Raspberry Pi. However, there are various example projects online that you could look at. For example, here is a blog post I found in a series about connecting a Raspberry Pi to a MinIMU-9 v5, which includes an LSM6DS33.
We also have this example code for the Balboa robot, which is a work in progress but contains code for communicating with the LSM6DS33.
You could also look at the LSM6DS33-related code in this MinIMU-9 AHRS example (by @DavidEGrayson), which is in C++ but shows how to write to more of the configuration registers, or our Arduino library for this chip.
-Paul