CS,
Yes, I usually mop the pig every half hour or hour (for a shoulder, I'd tend to do every half hour). Try to do the mopping fast so as not to let too much smoke and heat out from the uncovered cooker.
If you have some thick smoke rolling across the shoulder, the mop will tend to wash off a bit of the smoke. Don't fret over that. The smoke that you wash off will now be mixed in with your mop sauce and add to the flavor of it. And depending on what you've mixed in to make your mop sauce, the nasty look of it will intrigue your guests when you make up some mysterious ingredients you claim to have used in the mop sauce (lawn clippings, dirty river water, etc). Have fun with it!
By all means, feel free to put some of that mop sauce in with the shoulder when you foil it. If it is good enough to mop on a pig, it is good enough to cook in with the pig! Yum!
One consideration about using a mop sauce. If there is any ingredient in it that could spoil by leaving it outside beside a 200 degree cooker for several hours, either keep the mop on ice or inside when not being used, or else make sure none of the ingredients (such as chicken stock) are used that will spoil if left outside. Better safe than sorry!
So swab that shoulder and enjoy it! Let us know how it turns out.
Jim