Hide unconfigured games: Check this box if you don't want unconfigured games to be displayed in the main game wheel list by default.
PinballY always searches the "Tables" folder for each system to find all game files, whether or not you've set up the bibliographic information (title, manufacturer, year) and whether or not you've added any media items for the game. Normally, PinballY shows all of these files in the game wheel list. Games that haven't been configured yet are easy to spot because they use default background images and just show the raw filename in place of a title.
The point of showing the unconfigured items in the main list is to make setup easier, by letting you see at a glance exactly which games need your attention in terms of entering bibliography data or downloading media. However, you might prefer to hide these when you're just playing, or when you're showing off your cab to friends. Check this box to keep them out of the main list.
When the box is checked, you can still view all of the unconfigured games at any time, by selecting "Show Unconfigured Games" from the Operator Menu. That switches to a filtered list showing only the unconfigured items.
Note you can also explicitly hide individual games, using the "Hide Game" command in the Game Setup menu (reachable from the Operator Menu). You can use this to remove listings for files that you don't even intend to set up in the future, such as old backup copies or testing copies.
Enable underlay display: Check this box to enable the wheel underlay. The underlay is an image that's displayed near the bottom of the main playfield window, in the area where the "wheel" icons are shown. It's only there for cosmetics, to let you display a graphical backdrop of your choice for the game wheel area. See Underlay for details on this feature.
This checkbox doesn't affect Javascript access to the underlay. Javascript can still display underlay images even if you un-check this box. This box only prevents PinballY from automatically displaying an underlay each time you select a new game.
Underlay sizing: These settings control the layout of the underlay image. All of these sizes are expressed as percentages of the window height. You can enter the values with "%" signs, and they're shown that way for clarity, but the "%" signs aren't required; it doesn't affect the interpretation if they're omitted.
As with the other values, this is a percentage of the height of the window, so it effectively sets a maximum "aspect ratio" for the image. That is, it sets a limit on how far the image can be distorted by horizontal stretching.
The default setting for this value is an extremely large value, chosen to be large enough that it'll never be reached in practice. That makes it effectively an "infinity" setting, which is to say, no maximum cap at all.
Why would you want to use this? It's mostly for people who are running in "landscape" mode, like on a typical desktop PC, where the main monitor is oriented so that it's wider than it is tall. Pin cab users usually do the opposite - "portrait" mode, where the main monitor is turned so that it's taller than it is wide. In landscape mode, a normally proportioned playfield image only fills a narrow area in the middle of the screen, so stretching the underlay image to the full width would make it ridiculously stretched out. The maximum width lets you maintain a more appropriate aspect ratio. If you're using landscape mode, you might want to try a setting around 56.25% (9/16), since that will keep the image proportioned about the same as a typical playfield image.
See Underlay for more details on the underlay feature.