When the ships initially depart from base, their orbital parameters are set, and while drifting unpowered their positions will be known to each other and their base with a high degree of precision. Space probes like Voyager and New Horizon can travel for years or even decades and radio telescopes can be pointed with a high degree of precision to pick up their signals, even though their transmissions now are coming in with the power of a Christmas tree light bulb. So the two ships and the base can all communicate with high degrees of precision so long as nothing changes and the ships are in ballistic trajectories.
Once a ship makes a manoeuvre, it will be visible to everyone by its heat emissions and exhaust plume. The other ship and the base can see it equally well, and simply track the burn and calculate the new orbital trajectory. The ship and the base might have to use a slightly wider beam arpeture to ensure they account for possible errors, but once contact is made, the ship which changed trajectories can send a "handshake" signal which helps correct for any errors. Once again, the trajectories can be plotted with a high degree of accuracy so long as ships travel in ballistic trajectories.
To simplify things, ships might be told not to transmit to each other, but to the base, since the base is probably a space station, asteroid or moon which is easy to identify, and which has much larger and better optical equipment (much like the Deep Space Tracking network on Earth follows current space probes). The downside of this is messages ship to ship will take considerably longer, and this is a single point of failure which could cripple the fleet.
Of course since stealth is not possible in space, everyone will have seen the initial and subsequent burns, so know something is on a particular orbit, but with stealth and laser comms, won't know what exactly is out there.