Another idea is for the two vessels to fly along side the larger ship, with the pointy end wave-guides being outer-most to either side of the main starship.
Not a true cloak, but a way to disguise the vessels warp signature under the aeigis of placing less stress on subspace.
The result? A Soverign class that looks like a long range shuttlecraft or probe. as long as the two ships are on point along the galactic plane.