I'll add that the T2 "structural image" (usually a 3D volume, something like a Siemens T2-SPACE) alignment to AC-PC is useful if you find your scans getting pushed to the edge of the image space. I've seen images get cutoff during TORTOISE processing, where you might lose part of the superior parts of the brain. AC-PC alignment of either the T2 image or the template image will often take care of this.
I wouldn't AC-PC align your DWI images, TORTOISE will take care of that. And any changes you make to the DWI (outside of TORTOISE) would need to be reflected in the rotation or translation of the b-vectors.