Is this ok for upgrading?

Hi. I am manually upgrading to 1.3.9. I wanted to find out if uploading the new data this way is ok:

I am going into each folder in zc, clicking upload, selecting all the files out of my 1.3.9h zipped folder, and uploading them which does overwrite some of the old ones.

The only thing I have noticed so far is some old files not being included in the 1.3.9h files.....wasn't sure if these should stay or I should delete them out.

I am going into each folder in zc, clicking upload, selecting all the files out of my 1.3.9h zipped folder, and uploading them which does overwrite some of the old ones.
Not the recommended way to upgrade a live site - - Hope you backed up all files and the DB befor starting this in case??
The tutorial should be followed
https://www.zen-cart.com/tutorials/index.php?article=108
The only thing I have noticed so far is some old files not being included in the 1.3.9h files.....wasn't sure if these should stay or I should delete them out.
Remove them

yes I have a backup, but find the tutorials confusing and was hoping upgrading this way would still be affective. As long as I am thorough, will all the "holes" be filled from 1.3.8?

was hoping upgrading this way would still be affective.
Only dangerous if there are any issues

I guess I'll find out! My site was hacked and caused it to completely crash; so I'm hoping there aren't any issues elsewhere

My site was hacked and caused it to completely crash; so I'm hoping there aren't any issues elsewhere
There probably are and you should be doing ALL of the things to clean it
http://www.zen-cart.com/wiki/index.php/Recovering_From_Hacks

Oh yes I am also following the recovering from hacks page. I am having a hard time getting my passwords to change... I am hoping after I get the new files uploaded I can get them changed and saved without issues. Most likely I'll be back on the forum asking for help with multiple things! :D