No. Leave the cup there. And I don't know if I understood your question above, but if you look at the subframe at the front of the car, you can see where a good place to jack the whole front end is. Leave the cup in there and position the tabs on the cup so that the subframe sits between the tabs to help prevent the car from sliding off. (this is assuming your cup has tabs on it, both of my floor jacks do)
Any questions? Lemme know, I'm glad to help ya out.
EDIT: After reading your question again, here'* the answer to part 2: After jacking up the whole front end using the method above, place the jackstands in the factory jack points (behind the front wheels, on the unibody lip. There should be a small notch in the metal, that'* where you want to put the stands). The only time you wouldn't want to use those points is if there is excessive rust around those spots. If that'* the case, set the jackstands under the rear subframe mounting points, or elsewhere on the subframe, depending on what work you're doing.
If you need pics, post a request here. I don't have any handy, but can easily take some, or I'm sure that another member has pics of the areas I'm referencing.
'94 Bonneville SLE | 266K miles
CAI - K&N cone filter - polished intake runners - 140 amp alternator - 2.5" exhaust - Magnaflow hi-flow cat - Magnaflow dual outlet muffler - 106K on engine and transmission - Sold 1/14/07
94 VW Jetta - 151K - 2.0 - 5 speed - Ghetto black steelie wheel mod - Techtonics 2.25" cat-back system