Yes, these rituals are very sacred and effective for clearing negativities and obstacles but they also cannot simply be done or recited by anyone without the proper training, visualisations, meditation and in some cases, you may also require initiation to do them.
Sometimes we can sponsor qualified sangha members to perform these pujas on our behalf, but even then it is usually by the recommendation of our Lama or through methods such as divination. We do not simply just prescribe pujas to ourselves!
Actually, if you rely on Dorje Shugden sincerely and practice sincerely, this is very powerful to protect you and purify negativities. What DharmaDefender said is very good - have strong samaya (a clean, good relationship with your teacher), and take refuge strongly, hold your refuge vows well. This is the best protection there is because it protects you not just from immediate, outer negativities, but also protects / stops you from doing more negative things that will create even more trouble /negative effects for you later. Dharma practice, when we do it sincerely, is the ultimate protection that we can create for ourselves.
It is not healthy to be completely and totally reliant on an outer deity to solve all our problems. The protectors like Dorje Shugden can certainly help us along the way, protect us and help to create conditions that will help us, but they cannot take away our problems completely. If they could, they would have done that already! We have our own karmas to answer to, which they Buddhas cannot just erase, so the best person to help us, is OURSELVES through our practice. This is the best way we can collect merit that will help us throughout our life and also to purify the karmas that keep causing us trouble!