If you are renting a bike from Manali, you might not be able to take your bike beyond Leh. For the number of days that your bike had been parked, most rental agencies will charge about 50% of the bill. You will however need to rent another local vehicle at Leh to go around. The same applied if you rent a bike from Srinagar.
The most economical way to bike through Ladakh is to rent your vehicle at Leh itself. Since no outside vehicles are allowed in Leh, this makes sense. There are several rental service providers in the fort Road.