Precursor or parent ion scanning is very useful in the mixtures which fragment to produce common fragment ions. Tryptic mixtures containing glycosylated peptides is included in this category, so yes, if you want an increased detection rate, you should use it.
As a rule of thumb when using MS-MS, the first analyser allows transmission of all the sample ions, whilst the second detects specific fragment ions.
The technique used will vary from lab to lab and furthermore, can vary between equipment. It really does depend on the protocol in place at your lab, so I can only give you a general idea. In my laboratories, we analyse the course trypsin digested mixture in MS mode to create a peptide map. The information gained may be sufficient from this first stage. If not, the next stage is to switch the Q-TOFMS to MS/MS mode. The protonated ions of the digest fragments are selected and sent through into the collision cell. The sample ions then collide with argon ions introduced into the chamber which result in the sample ions fragmenting. The exact moment of the argon injection into the chamber needs to be carefully calculated depending on the expected ions present and the lab staff are superb at working this out. The fragmented ions present are then analysed by the second analyser.
What you have at the end is a MS/MS spectrum showing all the fragment ions. An ion spectrum is then produced for each of the components present in the digest. The spectra are carefully analysed and the sequences compared to that in a known database. In general MS/MS is excellent at demonstrating phosphorylation, acylation and glycosylation in the form of post-translational modifications or otherwise.