If you are talking about connecting analog sensors to the Pepper inputs, you can still do that through the CV ins, but the full-scale input range is now 0-10V instead of 0-4.096 V as it would be on the regular Bela cape without Pepper. The input signal is scaled down via a voltage divider, so you may see some strange interactions if the output impedance of your sensor is above a few tens of kilo ohm. You could consider changing the resistor values on one or more of the Pepper CV inputs in order to accept a different input range.
If you are talking about I2C sensors, then there is an I2C header broken out to the Pepper PCB that can be used for that purpose.