In general, the above posters are correct -- scan every coupon, if the register accepts the coupon, accept it, that's the official overarching policy.
However, to be more specific (if I understand you correctly), a BOGO coupon (or buy two, get $5 off, etc.) counts for *both* items. So if you picture every item having two "coupon slots" (one Target, one manufacturer), the BOGO coupon fills the Target or manufacturer slot for both items.
So if you had two items you wanted to buy and one manufacturer BOGO coupon, you could only apply Target coupons to either of those after that, not additional manufacturer coupons.
Cartwheel is also in addition to regular coupons, it doesn't fill the "Target coupon" slot but acts more like a sale (when we change the price manually to forcibly accept a Cartwheel coupon, we use "Ad Match" to change the price rather than a manual coupon for the value). So you could get lucky and find a sale/deal, manufacturer coupon, Target coupon and Cartwheel for a single item.
The only "crazy coupon ladies" that annoy me are the people who are clearly and knowingly trying to defraud us (fake or unapplicable high-value coupons*) and the one lady we used to get who didn't speak English and would dump a bag full of over 100 wadded up coupons on my lane and try to get me to go through all of them to figure out which ones would apply. Her kids were always out of control as well while she was trying to get me to sort through her coupons. Eventually she either stopped coming or perhaps we banned her. But I have no problem working through a bunch of coupons, if someone has a bunch I normally just lay them out and do them as we go to make sure they're all good. Now that "Extreme Couponing" is over (I think) and we started enforcing a 4-coupon limit, it's gotten better. I also think companies are wising up as to how they print their coupons (we used to get a lot of people wanting 100 travel pouches of Tide for free because the coupon doesn't say you can't get $1 off of the $1 pouch).
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* Worst real but fraudulently used coupon was a couple years ago when there was a $30 coupon for a men's electric razor. The real razor cost $200 but people kept wanting all of our $30 razors for free (and this was before the 4-coupon limit) so we kept having to reshop them. Eventually, the fraudsters got smart and started buying the $200 razor with the $30 coupon then driving to another Target and returning it to make a $30 profit.