It sounds you have a deeper problem, perhaps related to IIS permissions or even unblocking the downloaded module. Many factors can be at fault and actual error messages are needed to determine or resolve the underlying problem.
First of all, did you backup your website and your data before installing the module? What module and what error message did you receive during the install? Did your store stop working after the first or second install attempt? Have you installed any other modules recently with or without success?
Having to FTP the dlls manually is only part of the install process and will surely cause weird behavior if database scripts are not run or desktop modules do not match the dlls. Was a backup copy made of your website and your data before FTPing the new files?
With a backup copy, not only can you determine what happened, you can also restore it to the previous state. Without a backup, you may end up starting from scratch, especially with item/customer/order history (although there are workarounds).
Alternatively, depending on the orginal error, a few simple tweaks may bring your existing module up to date. That is how DNN upgrades are designed.