Barring a site do-over (which will work better in the future), you can upload only your recently modified files, and do them all at once...
1. After you are done making changes to your files for the day, right click your site's name in your Files Window (the topmost folder in the list) and choose "Select".
2. Choose "Recently Modified" from the pop-up
3. Change the "Files Created or Modified in the Last:" field to 1.
4. Click "OK". This will select (highlight in the Files Window) all files modified for that day
5. From the Files Window click Put (up arrow icon)