Once you have you left and right images, it’s up to you to decide what to do with them next. I use an application called Anaglyph Workshop to convert them to red/blue anaglyphs. However, you will more than likely have your own method. It’s all good, and as long as the image works and it doesn’t cause discomfort, then you will have succeeded.
I often find that the resulting anaglyph is darker than I like. If this is the case, I open the left and right images in Photoshop and up the brightness, either by using a brightness or exposure adjustment layer. This may make the images look a little odd, but remember, we are attempting to compensate for an unnatural darkening when the anaglyph is viewed through filters which will make a difference to the apparent brightness of the image. Remember to keep the adjustments consistent for each image.
Remeber than the filters used in anaglyph lenses are incosistent - so what looks dark for you may be correct for someone else. You need probably a couple of pairs to check the images against.