How do you align embroidery designs?

What do you mean? Are you using software or are you doing it directly on the embroidery machine using the built-in tools? Refine the question.

I am using software.

What software you using? Every embroidery digitizing software has an Align function in the Edit menu.

I'm trying to align 2 colors in a patch without leaving too much space between the colors. I use Inkscape/ Inkstitch. [Difficult to figure out how to install the Inkstitch extension, but I managed it somehow. Linux.]

I made a file with both colors over each other. Bit annoying that both colors show black in Inkscape. Saved it as one color and subtracted the area of the other, then repeated the process the other way 'round. I hope it works.