Filezilla Permissions

Hey guys, I am new to wordpress and the entire website building process so please bare with me. I have setup my site through bitnami and AWS and I am using the Valenti theme. I finally got to the point where I wanted to start editing my theme .php files. So I downloaded filezilla and followed the steps I found on the bitnami wiki. After following the steps I was able to find all the header.php, footer.php, etc.. files in filezilla and I changed the permisions with no issues. The next day I wanted to edit my category page so I followed the same steps in filezilla but this time none of my files are appearing. Filezilla connects fine with the SFTP and everything there are just none of the same files under the apps folder like there were the day before.

So if anyone knows what I could of changed or how I can change these file permissions that would be great.

Thank you,