I cant FTP to the boonex installed folder.

So, I can modify files and manage them from SSH but I cannot upload, delete, update files within the boonex installation over FTP. 

550: Permission Denied

I assume it has something to do with permissions set from the boonex install, any ideas?

My guess is the sites files are owned by an account that is different than your FTP account. Did someone else originally install your site with different ftp credentials?, or was it done with SSH under the root account which would be a big no no.

In any case my guess would be ownership issues. Similar to permissions, but not quite the same.

Would this fix the issue?

chown -R apache:apache [SITE ROOT DIR]

It was installed by me as root in that directory. 

Apache would not be the proper owner. The files should be owned by the FTP account, However some of them would be owned by the webserver which would be files that were uploaded by members such as photos. But the rest must be owned by the ftp account, normally the same account as the one used to log into cpanel. Unless you dont have cpanel.

I am running off of zpanel on a virtual dedicated server from wable (decent for web stuff, but it takes a crap ton of customization to get Dolphin working). This is proving to be a lot more work than I thought it would be. I tried changing ownership to apache:apache which seems to have worked things out.

What risks are associated with this?

This sounds more like a PC problem stopping you from writing files. 

Try using SFTP instead of FTP as it should help solve the problem. 

Your problem is your PC is not accepting file transfer via an unsecured connection thus being FTP in this case. 

Here is a link which should help you use SFTP which should help towards solving your problem.

https://docs.oracle.com/cd/E26502_01/html/E29001/remotehowtoaccess-14.html#remotehowtoaccess-40629

This one will explain more on SFTP

https://docs.oracle.com/cd/E26502_01/html/E29001/remotehowtoaccess-14.html

Your problem is actually a Microsoft problem which in some cases they may have a patch to fix it but not always. 

Note not all commands can be done using SFTP but you will find that between the 2 FTP and SFTP you will be able to do everything.

GL. Cheers

@ phil1ooo, I saw that, but if the 550 error were the microsoft issue (which I investigated) than it would be across all files and folders on the server. This was only inside of the Dolphin site. It seems to be resolved now that I changed the ownership to apache:apache. I will keep you all posted on if this is a fix or not. 

here if your not sure on how to use SFTP using FilleZilla I managed to find this which should help you out.

http://www.servermom.org/using-sftp-to-upload-and-manage-files-on-your-server/327/

GL, Cheers

Using SFTP now. I think that changing everything to chwon apache:apache fixed everything, but I would still prefer to have a private connection.

Thank you!

Your server should have a separate user account. Using Apache is dangerous as it has the potential of giving a hacker access to the files though the webserver account which if a security hole is found in apache, your sites files become vulnerable to attack.

You should have a separate user account for your website and all the files should be owned by that separate account. It is risky to have website files owned by root, apache or any of the other service accounts linux systems normally have.

 When I upload using FTP the owner shows as apache. That is why I changed everything. I think I might be missing something here. I don't like the idea of having a security issue :( Any ideas on what to look into?

Using apache is not the right path, using SFTP only means it's a more secure path and also apache will let you work through SFTP over FTP as it sees FTP as being insecure which is why it denies you access.

Now the only way around that is for you to create a new user group giving that group full access rights. Once that group has been created you will only use that group to login and work. That is the only other way around your problem.

The other option is to start from scratch on a cPanel server.

All the links I gave you explain all that and show you what to do. Use them and your problem will be solved, don't and you will be pondering on this for ever.

Cheers