The second one is incorrect, as you are asking just for wine glasses (empty, no with one).
The first one would be correct, but it needs some changes. First, let me point out some important things:
1.) The o (を) particle can't be used after the numeral "futatsu" as を marks the object of the sentence. Hence that the object here, is "wain", futatsu no gurasu
being the counter. If you didn't have aka wain before it, and the sentence would have started just with "futatsu no gurasu", then using を after it would have been correct as the new object would've been that whole structure => don't use wo on counters/adverbs/adjectives that follow the actual object.
2.)Futatsu no gurasu is a bit long and cumbersome. You can use the counter for glasses of liquid ~hai => it's easier to say: nihai instead of futatsu no gurasu.
Therefore, a correct version of the sentence would be:
*Aka wain o nihai onegai shimasu (あかワインをにはいおねがいします).
Or the long way: Aka wain o futatsu no gurasu onegai shimasu
If it was known before this sentence that you were talking about wine, you could've then shorten everything to just: De wa, futatsu no gurasu (or nihai) o onegai shimasu.
Hope this helps a bit :)