1. The Juubi is the sum of it's parts. Since Obito could control the sum of it's parts ( which were the Bijuu ) with his Rinnegan he forced the Juubi to merge with his body with his Rinnegan ability, thus becoming the Juubi Jin ( that's what I think anyways ).
2. Naruto due to his ability to sense negative emotions knew that Obito was most likely up to something so he tried to tell Sasuke to stop but Sasuke ended up proceeding anyway.