Use Selection mode for the feature layer. Set your symbol using Layer.setSelectionSymbol(symbol). If you have a complex symbology, set the renderer instead and leave the selection symbol blank.
There are two ways to go about the next part.
Use the checkboxes to composite a complex query. For example, if each feature has a unique identifier (call it IID), then you query will be:
Where the list of IDs is built from all the checked check boxes. jQuery can be very effective in building this list. Whenever a checkbox is updated, you want to execute
Use simple queries to add and remove each feature individually as boxes are checked or unchecked. When a checkbox is checked, you use:
When a checkbox is unchecked, you use:
As you add features to the current selection (or create a new selection) those features will be displayed. As you remove them, they will be hidden. Since selectFeatures() will execute client side if possible, this actually operates very quickly.