Well, let's use missiles.txt as an example (overlay.txt works similarly, but the columns have different names...once you figure it out for missiles, you'll be able to identify the columns you need in overlay.txt for the spells that use overlay graphics).Anyway, let's say that you wanted to change the missile for the sorc's Firebolt into the missile used for the Unravler's Unholy Bolt.
Go to the CelFile column and AnimLen columns for one of the Unholy Bolt rows. Copy them.
Paste them over the CelFile and AnimLen columns for Firebolt.
That is, in a nutshell, what you do. (AnimLen is very important. If set too high for the animation file in question, the game will crash...in the overlay.txt file, though, the column that is equivalent to AnimLen in missiles.txt seems less important. I have yet to crash even when I set wildly "incorrect" settings for that column in overlay.txt [I don't recall the name of the column...I think it's "Frames"].)
Now, complications can arise. Sometimes, the missile you change may have transparency turned off, which might make the missile look odd and not at all like the original. In this case, go the Trans column and set it to 1. This will usually solve the problem. Sometimes, however, turning off transparency looks cool for missiles that are normally supposed to have it "on."
Other problems and crashes can sometimes occur, and you simply have to deal with them as they come.
There are many unused missile graphics in the .mpq files. The datafile that comes with MPQView might not show them, though. Use my diabdata.txt datafile, which is avialable from Phrozen Keep's Tools of the Trade section right underneath MPQView.
Note that some animations are in subfolder, like the expansion pics, in which case the filename is preceded by expansion/. You'll see what I mean if you look at the missiles for expansion skills and expansion monsters in the missiles.txt file. Likewise, the unused animations for missiles (in the d2data.mpq file) are mostly in a subfolder...whose name I cannot recall. But you'll see it in MPQview. As with expansion animations, the subolder name would need to precede the name of the animation file.
As you will also see, you don't need to include the .dcc extension when you put the filename in the CelFile column...just the name of the file without the extension.
The folder for overlay animations in the d2data.mpq file also has several unused animations.
When you use unused animations, you won't automatically know what the correct AnimLen value should be. If you cannot figure out the number of frames (which I think you can figure out using the CV5 program), simply set AnimLen low, like to 6...and gradually raise it until you see "complete" animation (or complete enough for you) or until you crash the game (which is when you know it's too high...AnimLen values that are too low will not crash the game...they just might make the animations look less than stellar).
I believe you can also use overlay graphics in the missiles.txt file and vice-versa. Just make sure you include the path in the CelFile column, which I presume would be something like overlay/whatever/whatever/etc./etc. You'll have to experiment with this a bit or ask someone else to clarify/confirm for you (DigiBO knows the answer, I think).
It is also possible to extract monster and other .dcc animation files and use them as missiles. For example, I extracted the Gargantuan Beast's neutral (NU) animation file, resaved it as beastover.dcc, saved it to the path for overlay files in the patch_d2.mpq file, and then put beastover in the Filename column in overlay.txt for the Paladin's Might aura. I fiddled with the Trans column a bit to make the beast graphic nice and ghostly.
Hope that helps. 
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- JEFF
"A hero is no braver than anyone else. He is only brave five minutes longer."
For my latest mod (for LoD/expansion), download Version 1.1 of Sanctuary in Chaos
- Or for old stuff (for classic D2), visit my orignal mod site at www.planetdiablo.com/sanctuary