Long URL's showing in Browser

Hello,
I am new to Joomla and working on a website for a client. It seems as though we are having an issue with Long URl's showing up in the browser.
I checked the Joomla forums for an answer and everything seem to point to setting the SEF in the Global Configuration and changing the .htaccess files. After checking to see if both of those things we set correctly, we were still having issues with the urls not being SEF. After a little more investigating and having no luck with getting it resolved I reached out to the hosting provider to see if it was a setting that was possibly blocking the settings from being executed. Below is the response I received, If they are correct in what they are saying is the solution, How does one edit the Menu URL's? Thank you in advance for any insight to their answer.

Joomla Version: 3.4
FLEXIcontent version 2.2.1 rc

Siteground Response:
"I have checked and the SEF URLs are properly enabled on the site and they are working:

While inspecting the sites menu using the Chrome Developers tool however I noticed that the menu items are hardcoded to load from:

/index.php/site_content/your-content

This present in all of your menu items currently which is why you are left with the impression that they do not work.

My suggestion would be to check the extension you are using to create the menus and edit the URLs for the menus since I noticed that you are not using the default Joomla! menu builder."

first j3.4 + flexi 2.2.1 isn't good mix
you need to update flexi !
url is create by menu link in joomla you need to creat link
but can you provide an url example ?

Hi and thanks for the reply. Below is an example of a url in my browser:
justfrancesales.com/index.php/site_content/2-jfs/66-newlistings

you need to create link menu to your categorie to remove site_content

So I followed these instructions on how to add a menu link. The only issue is that I don't see an option to use the external link. It's does not show up as one of the option.

Select Menus → [name of the menu] from the drop-down menu on the back-end of your Joomla! installation (for example, Menus → Main Menu). Click the New Toolbar button to create a new menu item. Click the Menu Item Type Select button and then click the External URL Menu Item link under System Links.

Seems to me that there's an installation issue or a corruption of the plugin. I also tried to update the plugin to the latest version and it broke the site. So I had to reinstall the old version for the pages to work.

flexicontent doesn't use external link .....
create a link to category or item (flexicontent type)