Using Ultra Sonic Cleaner to Clean and Clear Crystals??

[Aion]

I think I may have read that incese and sage smoke can also cleanse crystals.

Yeah those can work well too, although it would depend on the kind of incense. Some will just 'colour' the energy rather than cleanse. Sage is the classic 'smudge' plant, but something like Palo Santo would work well too. I have found, personally, that cleansing with smoke is harder to smooth out heavy distortions but works for well for any light or outer layer work.

In your opinion should crystals be seperated? Like is it ok to keep them all together in a box or not?

Sure as long as they have all been cleansed first, which you should really do with any new stone you get. (Unless of course you got it from someone with a particular charge and you want to keep that, like a gift that has been blessed.) Things that are positively charged I wouldn't worry about, although some stones don't 'get along' with other stones. Mostly you want to be careful not to mix any heavily distorted stones in with cleansed one. If any of them feel 'off', cleanse them all.

Stones that you have charged in a particular way should be kept separated from other stones so that their charge doesn't dissipate or spread on to others. (Unless you want it to, I suppose.) Such stones should also be kept away from pure elements as that may alter their charge. Cloth, wood, metals, ceramics, glass are good containers. Wood and metals might alter or amplify the charge somewhat but mostly only while they are in proximity. Of course plastic is also nice and neutral.