While it is impossible to say for sure in which manner he is helping, I am sure a few phone calls have been placed. Barack Obama is the Commander and Cheif of the United States and his voice ultimately matters. If the FBI is investigating Clinton and he were to get knowledge ahead of time he would likely peak to the Clinton people regarding the issue.
President Obama is helping out Democratic nominee, Hillary Clinton, but he is not directly responsible for helping Clinton avoid her email scandal. Instead, by supporting her and the Democratic party, he is indirectly (with his support) helping voters look past the scandal rather than have the FBI not look into the email scandal.
The President is a Harvard graduate and not an intellectual slouch. He realizes like the rest of us thinking humans that this is a politically motivated lynch job that has gone awry. He is endorsing her because she is the most qualified, hands down. This woman has been First Lady, a senator, and secretary of state. No one else has such a resume, so no matter how much they vilify her she just keeps marching forward breaking all kinds of barriers.
There is no evidence President Obama is helping Hillary Clinton avoid an investigation into her personal use of e-mail while Secretary of State. Republicans would be all of the issue if that were the case. He has stated he will let the government agencies do their work, and nothing has come out to refute this claim.