Okay, I've tried the methods that have been suggested thus far, copying the files I want and using them to overwrite the existing files, and have been met with only partial success.

I've tried to include a couple screenshots to illustrate my problem, but apparently I can't even do that

This is what I want to have:

Conquest Texture Pack by Monsterfish, with
Dragon Windows from Conquest Pack (found in the ctm>glass folder under the dragonglass subfolder)
Cobblestone Stairs from JohnSmith Legacy, which have no equivalent in Conquest.

I invite anyone willing to spare a few minutes to follow my procedure & tell me where I've gone wrong.

So as not to ruin my stock Conquest pack, I copied it to my Desktop & renamed it Conquest_RegEdit.zip
For the cobblestairs, I simply took the ctm folder cobblestone_stairs from John Smith Legacy.zip and copied into the mcpatcher/ctm folder of my Conquest_RegEdit.zip
For the windows, I copied the folder dragonglass from the original Conquest_.zip mcpatcher/ctm/glass to the desktop. There, I renamed it glass and copied that folder into Conquest_RegEdit.zip's mcpatcher/ctm, thus overwriting the original Conquest glass, with it's thin circular lines that I frankly find ugly.
For good measure, I then took the file 0.png and copied it to the desktop. There, I renamed it glass.png and copied it to the minecraft/textures/blocks folder in Conquest_RegEdit.zip

The results would be easier to see in screenshot form, but I can't figure out how to post screenshots to this forum without uploading them to a Flickr or similar account, which I neither have nor have the patience at the moment to make. As such, I shall describe the results as best I can in words. And those who have followed my procedure should be able to see for themselves.

In the case of the cobblestone stairs, the textures for the sides appear to have translated successfully. However, the tops of the stairs retain their original cobblestone texture, which is not what I wanted. Compare this to the original John Smith Legacy, where the tops of the stairs have a stone slab sort of texture, which is what I wanted, to match the tops of Conquest's stone fences, which have a similar appearance.

The windows were a complete failure. Only the 0.png texture, which I also used for the stock glass.png overwrite, has shown, with no connected texture effect at all. I experimented by creating a 3x3 section of glass panes, which with this texture should produce an arch effect, but instead just produces a wall of dragons & decorative lines.

So, friendly folk who have helped me so far, where have I gone wrong and what must I do to fix it?

there are different versions of ctm with different textures and different configuration systems

delete the old stuff and them copy over the new stuff including config files
if that does nto work you will need to look up the ctm version and config system

In the /assets/minecraft/ folder in the zip there is a folder called "mcpatcher", that's where all mcpatcher textures go. In it, there is another folder called "ctm", that's where you'll find the textures you want to edit. I don't know if the textures you're going to substitute are for ctm, if they aren't all you need to do is delete the "glass" folder in the ctm folder, or whatever texture you're replacing.

you should be able to find the image that the connected textures uses, rename your new file with the same exact name, replace the old file, and install the new resource pack. If the instructions weren't clear enough, I can go into more detail (if need be, other wise I hope this helped)