Unless we had the same hub/axle set up we really can't tell you the combo of spacers and nuts you have, but here's what I do.

I set the cog/RH side first. I use however many spacers/washers with cone and lock nut (and some hubs have a second/inner lock nut too) to achieve the freewheel seat to end of lock nut dimension that works for the freewheel you have. For the typical Asian made freewheel in 6 speed (as example) that dimension is about 34mm (IIRC), this can be test fitted later with the LH side assembled, the bearing adjustment close to correct, the freewheel mounted and the wheel in the frame so a chain can be placed on the small cog and large ring to confirm RH seat stay lower inner end clearance WRT the chain (and remember that the chain kicks up slightly when shifting off the small cog). Whatever is left (spacers/washers) over goes on the LH side.

This gets you the least amount of RH offset and thus the least wheel/spoke dishing for the strongest wheels. If the resulting rim's location (WRT the frame) is too far to the RH side it could be dished over to the left or you could try less RH FW seat to locknut end if you can without the chain contacting the stay end. Or you could transfer some spacers/washers from the LH side to the RH side.

In the future only take off the axle one end's cone, spacers/washers and locknut. This way you have the OEM set up maintained. This stuff is all about tinkering and trying various arrangements. Lastly don't think that the original set up was the best one of even had the rim centered and the chain line proper. Andy.