Your getting confused with the terms.
Check in and out is not upload and download!
when the file within any document library that is checked in than its locked to all users. You cant make any ammendments to the file and its in public view. At this point if you have the right access you can check out the file. When you check out there is now a lock in place where no one else can check out the file as you have it, think of it like a door and the file is the key. when its checked in the door is closed and the key is in the door. When you want to make ammendments to the file you check it out (open the door and take the key). No one can make ammendments as you have the key. When you check in the door is closed and the key is available for anyone else who has the privlages to take the key and do the same. This is so you cant have two people makeing ammendments to the same file at the same time.... only one person can make changes at any given time.
when checked out the file can be ammended if it is a file or properties on the library can be changed. When checked out you can then download the file to your local drive make the changes and then upload it back in to sharepoint library. Once uploaded you check the file back in so others can use the file and can see the updated changes.
you can as others have noted do it in sharepoint designer or the method above as this would also be true if the feature is also enabled on a document library that stores pdf's,word docs ect...
1) checkout file so you only can make ammendments to the file at that given time:
2) as you can see the file is checkout out now so i have ownership of the file and now i can download the file for ammendments:
you can discard the checkout if you want to make it available (public access) or check in.
in your case you want to update the file.
3) download the file to your local drive:
click on dropdown -> send to -> download a copy -> select the location you want to save on the local drive.
now make your ammendments to the file.
4) once complete and you want to update the file on sharepoint with your new changes you need to upload first and then check in and publish for everyone to see updates.
so the above images are for 2010 but i know your on 2013
this image shows the ribbon that you can see has all the options in one location just do same as above!
1) select the file
2) check out
3) goto the file drop down and download / sometimes you can just click on number 6!
if downloaded file:
4) once done upload file back in
5) check file back in
if clicked on edit button (6)
4.i) make changes
5) check file back in