The advanced settings of EWWW really let you customize the plugin for your specific site and for your unique workflow, and additional settings are available in the Overrides.
JPG Quality Level
EWWW lets you change the default quality used by WordPress for image resizing and thumbnails, and this will also affect PNG to JPG conversion if you enable that. Additionally, this setting impacts the compression quality when resizing uploads using the Max Width/Height settings, and the quality level for WebP images. The default in WordPress is currently 82, and I recommend you stick somewhere between 70 and 90 for optimal quality, but you are free to use any quality level you want here. You can read more about JPG quality and some common misconceptions in a related article (scroll to the bottom).
This is not a user configurable option, but it is worth explaining how background optimization is enabled (or not). When you first activate the plugin, it will send a test packet to see if your server supports background optimization. Essentially, the server is sending a packet to itself, but some security plugins don't allow this, so that's why the plugin has to verify that such a request will work. If the packet is received, and has not been altered, the background optimization "option" is automatically enabled. There are still some cases when it may not be used though. First, if you use the Shield security plugin, and have the option to lock a user's session to a single IP address, background mode will not work. Also, when converting images, background mode is not used. When converting, this is so that a contributor doesn't accidentally insert the wrong image into a new post or page. When resizing options are enabled, the resizing will be done in the "foreground", so that the plugin can determine where an image came from, and which resize restrictions should be used. After resizing, the image will be optimized in the background. Both of these behaviors can be overridden by a developer using the add_filter() function in WordPress.
Another option that can be used to speed up optimization is parallel optimization, which allows the plugin to do up to 5 images at once for a pretty good speed boost. This option will be ignored if background optimization is not enabled, or if you have less than 6 resizes being generated per upload and are not using the API.
EWWW IO has a folder scanning feature that will look for images from your theme, and a handful of pre-configured folders for plugins like buddypress and meta-slider. To make sure these images are optimized regularly, there is an option to schedule optimization of these images on an hourly basis. The plugin will ignore any previously optimized images.
Include Media Library Folders
If your theme or some plugin is generating images in the media library folders, but not registering them properly in the attachment metadata, you can tell EWWW to include the most recent 2 folders in any scans. This applies to Bulk Optimization and Scheduled Optimization. For example, if it is October of 2017, then the plugin will scan wp-content/uploads/2017/09/ and wp-content/uploads/2017/10/ and optimize any images within those folders.
Folders to Optimize
If you have images elsewhere in your WordPress folder, you can add those to the Folders to Optimize setting. If new images in a folder are being automatically optimized, then you only need to put the folder in here once, run a Bulk Optimize, and then remove the folder from the settings. You can verify what is being optimized by visiting the Bulk Optimize page, and clicking the Show Optimized Images button. Otherwise, when a folder isn’t being auto-optimized, you can leave the folder in this setting and enable Scheduled Optimization to look for new images every hour.
It is important to enter full file-system paths, not urls or partial paths. The path to your WordPress folder is given directly above the textarea for this setting as a reference point. So if it says /var/www/wordpress/, then any path you enter should include that "root" location at a minimum.
Folders to Ignore
When running a bulk optimize, the scanner searches for the same images as scheduled optimization in addition to the Media Library images, so if you want EWWW to ignore your theme, or some other folder, you can configure that here. It is not necessary to enter full paths for this setting, but any image that matches something entered here will be skipped. For example, if you enter '2015' because you don't want old images optimized, it will not just skip the 2015 uploads folder, but ANY file that might have 2015 in the name (which might be OK for you, but be careful with that).