Board Thread:Naruto Discussions/@comment-9782468-20170118003542/@comment-4080775-20170118050615

When you make clones, you split your chakra into said clones, BUT, that doesn't mean they clones can't regain chakra themselves over time. By having the clones elsewhere, they were able to recharge missing chakra on their own and gather natural energy to make Senjutsu chakra. Basically, Naruto and his clones together had more senjutsu chakra than naruto by himself could have had alone.