Hmmm...that's kinda tricky sounding, maybe not though.
A channel is basically the ammount of color or 'something' represented by black, or shades of grey
So if you open a completely red CMYK document and look at it's channels you would see the Yellow and magenta 100% black, because it takes 100% of each to make the red.
So that said, if you want to add a spot color, you would need another channle, a spot channel because it's a fifth color. You would get the spot color to go where you want by indicating on the channel with black, or if it's a gradient it would be a gradient of black to grey for instance.
So onto the bevel/drop shadow situation...and this is where you may be thinking to much about it.
A spot color would probably only be in a solid area or semi transparent. Either way, you could make a selection of the place you want the color and paste into the spot channel. you then have basically the place where spot is going to go. But if it's an overlay, then you would place the spot over an area where the bevel emboss already has been done.
If you really had to, you could do a bevel emboss, paste into the spot and you will have those now grey levels to differentiate the spot color, but remember there would be no black ink to really make it look right. this is why it's best just to go on top i would think.
So basically think of it this way, a channel is just a direction to say, hey, put ink here and how much...the other really cool thing a channel can do is be saved as a selection, so if you have an spot channel, you can save as a selection, load into the working layer and do some trapping off of that if you need, but that's a whole nother subject
Ordinary Life is Pretty Complex Stuff