Doing adjustment (highlight some words) in the PDF file through iPad but can't save the same file

Hello, there, 

I am a student using a lot of pdf files. However, every time I opened a pdf file from my icloud and I did some comment (highlight the words or put some notes), once I finished the work. I suddenly found out the file was not the original one I opened in the icloud. It would become another file saved in my pad.

It bothers me a lot~~~~~~ I hope I can use the acrobat app in iPad to open the pdf file and I can do the comment on the SAME file, not another new one in my pad, but the SAME file SAVED in the original place in my icloud.

I can do it in the PDF Expert but I can't do it in the Acrobat APP, but I have paid the money for the pro-version!! >"<

Look for help, thanks!!