This is the best method I have come up with in my experiments with seamless skyboxes:
This is an example result in action.****You'll need
this tiny program; it has a set of panorama-editing functions that we'll want to use. (Because a skybox is essentially a cut-up panorama.)
You'll also want to have an abstract brush on hand when you have to mask or clone-stamp; I use
this one. (Unless you're using photo reference (like me, in this case), and since I'm guessing you're drawing all of this manually - you probably don't need this.)
****First, draw your space-scape; we will be converting this image into an equirectangular panorama - this means all six of your skybox faces are already contained within this image, so make it large and
make sure the image conforms to a 2:1 width-to-height ratio (For example, mine is 4096x2048).
Offset the image (in Photoshop,
Filter > Other > Offset, make sure
Wrap Around is selected) by
half its
width to the right. (In my case, by
2048)

The fun part; clone-stamp/mask or draw on top of the seam in the middle of the image.

Offset the image again to return it to the previous view.
Next, save this file (reccomend .TGA) and open it in
HDRShop. Click
OK on the dialog box that appears; it doesn't concern us.
Go to
Image > Panorama > Panoramic Transformations, you will get a new dialog box:
1) Set the
Source Image format to
Latitude/Longitude.
2) Set the
Destination Image format to be the same.
3) Set the
Width and
Height to your image's existing dimensions (check Source Image dimensions if unsure)
4) Select
Arbitrary Rotation, then click on
Settings; input
90 for the
Z axis.
5) Uncheck
Use Bilinear Interpolation.
Click
OK; you will get an image with two prominent areas of distortion in the middle (
right-click > Zoom Out to get a better view), like this:

If you still have Photoshop open, (in HDRShop) go to
File > Edit in Image Editor, this will open the new image in Photoshop; proceed to stamp/mask away or draw on top of the distortions until happy with the result.

Save the file and open it in HDRShop once more. Again, go to
Image > Panorama > Panoramic Transformations.

Pick
Latitude/Longitude as the Source Image format, but this time, however, pick
Cubic Environment as the Destination Image format. Now, depending on the resolution you want for your skybox faces to be, input one of the following for the
Width:
1536 - for skybox faces that are
512x5123072 - for
1024x1024 (this is the one I'll use)
6144 - for
2048x2048 (not recommended unless your source image is
HUGE.)
Finally, click
OK. You should now get vertical cross cubemap configuration which you can cut up into six images and convert to a seamless skybox!
