How to upload the whole ZC program to the server, individual files or one ZIP file?

I use FlashFXP as my ftp program. I usually uploaded the complete ZC program to the server as one ZIP file and then unzip directly on the server. Is this the correct way to upload it, or do I have to first unzip it on my PC and upload all the files?

If I unzip the ZIP file on the server and later retrieve the files for editing, I get an a message from UltraEdit asking if I want to convert to DOS.
I thought the FTP program, in this case FlashFXP, was supposed to do the conversion of characters from Unix to Windows. Is this normal, anyone else experiences this?

If I upload the files individually instead of a ZIP and later retrieve them from the server to edit them, I do not get the message from UltraEdit asking me if I want to convert it to DOS. This makes me think FlashFXP is not making the conversion, am I right?

If you load it to the site and unzip it is faster as that is a smaller file to upload than when unzipped ...

When I work on Zen Cart ... I set up my computer to have:

c:\websites\zencart_v1302

I unzip Zen Cart v1.3.0.2 into that directory ... and to make my life easier, I then make a directory called:

c:\websites\current_shop

This way my current shop is somewhere I can find it ...

Now I have on the left side of FlashFXP

c:\websites\current_shop

On the right, I have my shop:

/public_html/current_shop

This lets me set up my bookmarks in FlashFXP so I can navigate around my site(s) faster ... and don't have to reset thing all of the time ... a quick rename of directories manage that type of thing for me ...

I may have a dozen sites setup like this or 3-4 versions per site depending on what I am doing ...

I open the files with UltraEdit on my computer and do my work, then rename the file on the server and upload my changes ... never can have too many backups ... :cool:

I never edit the files directly on the server ... I find more evil than good comes from that ...

Hope that helps you a bit ...