Your sub albums are listed just below the upload area. Click on the one you want your images to go into to switch to it, before you set up your upload. That should get them in the right place.
For images that you wanted to go into a sub album, but didn't (or that you decide to move later) you can do one of two things:
[a] You can click on "move" just above the image, and you'll be given a drop down from which to select the sub album you want to move it to. Then click on move, and you're done.
[b] If you have more than one image to move to the same sub album, you can click on the checkbox just below each image you want to move, then scroll to the bottom of the page, and click on "move selected", and you will be given the same drop down as in [a] and can proceed from there. (If you want to move some images to one sub album and some to another, you'll need to do as many operations as sub albums.)
Whenever you move images you will be warned that doing so will break any links you have made to them. So, if you have already posted an image link and then move the image, the link will no longer work, but you can fix that by substituting the new IMG code.
Hope that's helpful.