I'm not sure what synth programming parameters Atmosphere gives you, but what I would do if possible is to isolate each tone as you have done and then reverse engineer it and apply it to the Virus. Should hopefully be easy enough as you have the patch, albeit on Atmosphere.
Dismantle the Atmosphere tones individually in reverse order: Take off any effects, then take off any unison, then zero any sources/destinations in any modulation matrix, zero any amp keyfollow, open wide the amplitude EG (instant attack, medium decay, maximum sustain, no release), then zero any LFO destinations, followed by dismantling the filter - zero any filter balance (if there are two filters being used) as well as filter keyfollow, then open wide the filter EG (instant attack, medium decay, max sustain, no release), followed by zeroing resonance, and open up cutoff to maximum - then dismantle the oscillators - zero any pulse-width, oscillator sync or similar, then zero any semi-tone pitching, followed by fine detunes.
You should be left with just the raw oscillator waveform(s), completely dry.
Isolate each waveform. Then go to your Virus, go to the Init patch (initialised) and try and emulate these waveforms using the oscillator section. Try the Virus's PCM waveforms if necessary too.
If you manage to get something you're happy with, then you can simply retrace your steps in the reverse order that you dismantled the Atmosphere patch, one step at a time (by hitting the undo button each time, if there is one), emulating the oscillator pitching, filter, filter EG, LFO, Amp EG, etc. until you finally get to the effects again, applying similar settings/modulations to the Virus patch at each stage. It has to be done by ear (as you can't just simply translate parameter values), and may take some time, but it can prove very fruitful.
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PS > And another thing! Will the Ti|3 have user customisable/importable wavetables?  A ribbon-controller or XY-Pad might be nice, too, please! Thanks!
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