You need to replace both switches or render one of them inoperable.
In the case of a 3way circuit where two switches control the same light, the Zwave switch needs to replace the second switch so that it may directly control the load and the auxiliary switch replaces the first. Both also require power all the time which means one of the traveler wires must always pass power from the first switch location to the second, so the circuit cannot act as a typical 3-way.
This is circumvented by using the auxiliary Zwave switch to wirelessly transmit to the switch controlling the load. To achieve this, you must “associate” the two. This cannot be done by the 2GIG panel and is the reason you must use the minimote.
Or…you can completely bypass one of the switches and render it inoperable and just pass power behind it.