There’s a difference between the uses of the Confederate battle flag and the government (civilian) flags. For infantry, it’s a version of the battle flag (Army of Northern Virginia was square and the size depended on the type of unit - large for Infantry, smaller for both cavalry and artillery; Army of Tennessee was rectangular). These are the flags that can and should be used for Confederate veterans.
The civilian flags (after the Stars and Bars) was the battle flag in the union and a white field, as Steven mentioned, and later in the war with the red bar on the fly end. These last two should not be used for veteran profiles.
While there were other military flags of various types, some using the Cross of St. Andrew, these were not widely used.