A not guilty plea is a denial of the charge and none of your constitutional rights are waived unless you expressly wish to do so. You are presumed innocent and the prosecution must prove your guilt beyond a reasonable doubt at a subsequent trial.
After your arraignment, the next hearing will be a pre-trial hearing where the prosecutor will be present. You and your lawyer are required to be present. It is not uncommon for a defense attorney to continue this hearing once or more to allow sufficient time to investigate your case and negotiate with the prosecutor. This also allows the attorney to find out more information about possible diversion options that could help you keep the crime off of your record. At a pre-trial hearing, motions may be heard and a jury or bench trial may be set. Information about all evidence in the case and witnesses names is exchanged.