If the gbox and the transfer case are both out of the car, then put the gbox into any gear, grab the shaft in the bellhousing turn it a little and then see if you can close the gbox and transfer case up together. This is just about getting the splines of the 'connecting shaft' between centre diff and transfer case. It's the hollow tube that connects the two assemblies.
If the transfer case is still bolted to the back of the engine, and you're trying to attached the gbox to the engine/transfer-case, then you obviously can't get your hand into the bellhousing to turn the input shaft of the gbox.
In this case, you need to be able to turn the rear drive-shaft (if the rear wheels are off the ground), or unbolt the driveshaft from the transfer case and rotate the flange on the back of the transfer case. This should get the splines lined up.
peter