It's a little button battery, like in a watch. It'll be on the motherboard. They either look like this, or may be standing upright:
http://pctechnotes.com/wp-content/uploads/2009/09/remove-battery.jpg
Make sure you replace it with a rechargeable one (any local computer store should sell them), or it may cause damage to the system.
If by cover you mean the heatsync and fan, then before re-attaching it you will need to remove the old thermal paste (the gloop that is on both it and the processor) very carefully. This guide will show you how:
http://www.bit-tech.net/hardware/2009/02/16/all-about-tim/4
In place of the cleaning solutions you can use rubbing alcohol, provided it is more than 90% alcohol, preferably it should be anhydrous.