Information about antenna assignment probably comes from this page. Basically, most of Teltonika routers work as MISO systems, meaning that there are two receiving channels and a single transmitter.
Using two antennas with different gains will not necessarily provide better connection quality. Since both connectors serve different purposes, it is suggested to use MAIN connector with the antenna best suited for the environment: directional high-gain antenna, when router is far from the transmitter, and low-gain omnidirectional antenna, when transmitter is nearby.
If changing antennas is an issue, it is better to to have both connectors with omnidirectional antennas, as directional one requires alignment to a base tower and is preferred for stationary use cases.
These are general guide lines, however, if possible, it is highly recommended to test different setups in field, as radio signal distribution might be very uneven in various places and some results may not be intuitive.