Doesn't matter which side since of the manifold. Driver's side is easier to get to and drill. On the passenger side the downpipe and the starter make it difficult to get a drill in there.
You can drill it with the manifold still on. You'll lay under the truck and drill up. The majority of the shavings will fall on you (very important to wear proper eye protection) while you drill and tap. Than you can run a small magnet around the hole to get out any shavings that made their way in.
Be sure to be cool with the tap as you are tapping the hole. If you force it forward to cut the threads it's possible to have the shavings get the tap stuck in there. It's best run the tap in a small amount and then back it out, clean off the shavings,etc.. Then continue going.
Hope this helps.