Hmm... Rayquaza is Lv. 70, right? Catching that Pokemon would make it easier to finish the game in Pokemon League. ^^ But still... If you want to defeat it, use Blizzard or Ice Beam with your strongest Pokemon if you want. What I think is that you might need to catch Black Rayquaza if you keep reset the game until you got it, then use Master ball 'cause Black Rayquaza is definitey worth it. I think you have Pokemon around Lv. 50, right...? Hm... Let's see...
would be better to(in my opinion) use state save type(shift + F1/F2/F3/F4/F5/F6/F7/F8/F9 any of these would do when you load just press the F1/other F's mentioned) during the battle using only ultra balls and super revives(not using cheats just use all the miney saved up from the entire adventure...hehehe i rarely use my money during my travels anyway) in about ultra balls somewhere 30 and all types of non herbal revives at about 10+