/rg create [name]
/rg redefine [name]
/rg addmember [name] [player]
/rg flag [name] [flag] [value]

After you have built your spawn, select it with WorldEdit
Now type //expand vert (This makes your selection cover from y0 to y255)
Now /rg create spawn
That will make a region named "spawn". By default, the creator of the region and all players with worldguard.region.bypass.* or worldguard.* or are opped will be able to edit the protected area.
There you go, you've protected your spawn.
If you want to disable pvp, disable spawn eggs, or disable taking damage in your region then you should read on.

Once you've made your region, you may want to change certain properties such as pvp. You can do this with /rg flag [name of region] [flag name] [value]

The main flag you will change is pvp, you can do this with
/rg flag [name of region] pvp deny
or
/rg flag [name of region] pvp allow

depending on if you want it allowed or denied.

Some other flags you may want to change are:

tnt
invincible
mob-damage
mob-spawning

You can delete a region with /rg delete [name]
You can change the size of a region with /rg redefine [name] (The region will be changed to cover your current WorldEdit selection)