If you're doing a long-distance point-to-point wireless link over 802.11a, b, or g, then you just want the "main" (not "aux") antenna connector to have the high-gain antenna hooked up to it, pointed at the high-gain antenna on the other end of the link. Lock your equipment to using just the main antenna.
Update: Oh, you're using omnis. Read on.
If you're using omni-directional antennas, then shame on your antenna vendor for claiming that they're high-gain. I don't usually consider omni-directional antennas to be high-gain, despite how some vendors choose to advertise them. +3-9 dBi like most omnis get isn't a lot of gain compared to a directional antenna like a typical yagi.
Anyway, in the case of omnis, realize that they get higher gain in a 2-dimensional disc by sacrificing performance in the directions above and below the disc. Yes, it can be kind of confusing that "omnidirectional" doesn't really mean all directions, it means all directions in a 2D plane. An antenna that works equally well in all directions in a 3D sphere is called an "isotropic" antenna. In fact, directional antenna gain is measured in terms of how much more of the signal goes in the primary intended direction as compared to a theoretical perfectly isotropic (spherical coverage) antenna. That's why antenna gain is reported in dBi. That's deciBels referenced to an isotropic antenna. Think of antenna coverage patterns like a water balloon. A typical water balloon is basically spherical. But of you hold it and squeeze it in one direction, it extends in that direction, but contracts on the sides where you're applying pressure. So a directional antenna "gains" performance in one direction by sacrificing performance in other directions. An "omnidirectional" antenna gains performance in a 2D disc by squishing the top and bottom of the sphere. Think of a water balloon squished between two books.
If this is a single-story building or an outdoor application over flat ground, then adding a second pair of omnis isn't going to help much. But if you're dealing with a multi-story building or interesting terrain, then it could help to add another pair of omnis oriented perpendicularly to the omnis you're already using. That way you get more coverage in, say, the "vertical" direction, instead of just the "horizontal" direction.