Some rules will use the Battle Board - those with 4 or 5 man Bands in a skirmish setting. But for larger games with multiple larger units like NUTS and 5150 Star Army, you'll see that's for the tabletop.
Now just about all of the rules that use the Battle Board have Tabletop rules as well. If it doesn't, then download this freebie; a 4 page How to for Battle Board to Tabletop rules.
And Cover? Heck yeah, ALL rules use Cover; just check out the Shooting Tables; pass 1d6 or score a 8 or 9.
Hope this helps.