I have stock differential and replaced the cover with the Jegs, which includes a fill and drain plug. While filling it took much more than usual oil to fill. It's been a while, but it seemed like I added much more than normal. I then checked the stock fill plug, and oil came out.

Is it okay/better to fill to the higher level from the new cover, or should I only fill to the stock fill level? Will I hurt anything with more oil in it?

I used about four bottles. I thought it only took two the last time.

I would probably take out the stock fill plug but fill it through the cover just because its easier. 4 quarts is a lot.

Remove the stock fill plug and let the excess oil run out. Do not use the hole in the cover as a fill level. These covers have the hole too high and excess oil can cause foaming, which can lead to gear failure.

What brand cover did you buy? Is your axle a 9 or 10 bolt?

Sounds like the cover needs a redesign, if the plug that that high.

Thanks for the info.
I essentially drained the excess through the stock fill hole.