turn on at the old fixture using two separate switches. Your new fixture only needs one switch so you just didn't use the 2nd wire at the fixture and capped it off. Seems that the 2nd wire can still be made "hot" by turning on the second switch. This is not safe because you might have it "on" and someone working around the fixture might think it is abandoned--since it is capped--and could get a shock. I'd recommend the switch that is no longer used be removed. If you do that, you can leave the wire from the switch to the fixture that is no longer used in place since it will be dead and can't be activated. There will also be a "hot" wire that feeds power to the switch you are removing, so that wire will need to be dealt with. Most times, with two switches like that, there will be one wire coming from the breaker box to one switch and then it will just be jumpered over to the 2nd switch. Just remove the jumper wire, assuming the switch you are removing isn't the one connected to the breaker box. If it is, you will have to move the "hot" lead from the breaker box over to the switch you are still using.