quick question on where to add water?

I have a 1996 cobra and the temp light came on. when I checked the over flow box it was real low. I was told you had to add water by removing the plug off a tube that screws off. cause if you dont add it there you will get a air bubble. so I added a little water in that tube, but not much went in. so is it safe to add water in over flow box now?
 
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