Hello 2bForgotten,
When you have separate synchronized sensors it is suggested to use Multi-camera system approach. In you case:
1. Create a new directory and then two subdirictories in it. Call them "1-RGB" and "2-IR", then put the images to each folder coming from the certain sensor - the order of the images in the folder should correspond to each other.
2. In Metashape interface use Workflow Menu -> Add Folder option and point to the "master" directory created in the beginning of the previous step. In the Add Photos dialog shown shortly after the folder contents are analyzed, select Multi-Camera System approach - > "Create sensor from each subfolder" option.
3. After loading images go to Tools Menu -> Camera Calibration dialog and, if necessary, enable "Reference" option for the slave sensor. In case the offset between the sensors cannot be neglected, then enable also "Adjust location" option. Additionally make sure that Layer Index in the Bands tab is different for Master and Slave sensor.
Approach would work if the sensors are synchronized and their relative exterior orientation doesn't change during the capturing process.