Hi, wait til spring, get it into a large pot of the clay plus ~ 20% perlite (to keep it light), and 20% 1/16" size bark bits (mulch?) all mixed together, with no pebbles or crocks etc. on the bottom - just the plastic canvas square to cover the hole(s). It'll need to grow for at least 3 yrs before it begins to do much of anything, though if it doesn't show any trunk 'movement' (vs ramrod) you could always use loose cord around the trunk, attached to the pot sides, to create some shape while you wait for fatness. If the top gets too bushy, trim back long branches, but keep lowest ones (at least for the indefinite term) as Gingko doesn't 'bud back' below where you've cut and the lowest branch especially is responsible for growing out the trunk girth. What I'd suggest is that next fall, after keeping the tree outdoors the whole summer (from May 1st) you sink the whole pot into a large container of mulch and top it up about an inch or so above the rim (no watering once the soil freezes hard tho'). Your tree should be ok that way as it really doesn't belong in the house anyhow and needs cold dormancy to survive in future, but for this season leave it inside in a cool, airy and bright place. Don't repot until April, now is not the time unless what it's in is too small, in which case try to get the whole thing out in one piece (hand over top) as much as possible and into the new pot/mix already filled to an appropriate height for the rootball to sit 'on' while you then fill in around it.

Also, once it's in the new mix, you can water without being afraid of roots rotting as it'll come out the holes quickly - do it when the top 1/2" or so is dry, and don't let the pot sit in drain water unless it's raised above it on pebbles. Take a look at http://www.xs4all.nl/~kwanten/thetree.htm to learn all about your tree, and get more bonsai advice.

Isn't 3 months old too young to bonsai?

Ryan... read the second line of my note...

Oh wow. Hahaha, I am so bad at that.