Any of the hotel roof top bars like J-6, Altitude, Hard Rock Hotel roof top, Se Hotel roof top, the W, or even Stingaree. And if you have friends who are bi, and who want to go a more gay/bi friendly bar, then there's Hillcrest neighborhood right up the 163 from downtown, where the major bars there are Mo's, Cantina's, and Universal. And in University Heights - Lei lounge, and Bourbon Street. Lei has some awesome cocktails and food and it definitely caters to a more sophisticated crowd. Lei lounge has a really mixed crowed of gay and straight peeps. But for downtown, I would stick to the bars I mentioned in the beginning.
My top pick would be Altitude on the roof of the downtown Marriot on 6th and it doesn't have a cover. You can see the whole city from up there and at night they have a DJ. But all the roof top bars are cool. J-6 also doesn't have a cover. For Stingaree, you can go to clublistnow.com and put yourself on a list and should - otherwise it costs like $20 but its a really amazing club. For the other bars I listed, after 9pm, they all have covers around $10 on the weekends.
All these places can be found on Yelp and other review sites. Have fun in San Diego!