Simon,
If the bike has been out of use for some time, the oil may have drained from the tank into the sump, and often, the return pump is not large enough to quickly pump it back. As you have already had it running, plenty of oil will have been distributed around the engine, so it will be safe to remove the drain plug from the sump and drain all of the remaining oil. Replace the plug and top up the oil tank. On restarting, it will probably still smoke until the excess oil has been burnt off. Also, the rings may be gummed up, so several cycles of running it and then letting it cool may be needed before the rings free up.
Regards,
Eddie.