There are no right or wrong ways... but instead many different ways that will usually get you to point B, regardless of what you choose... some paths just take longer than others.
There are certain advantages that PT 141 schools have. Usually they are larger meaning that they have more resources in terms of aircraft, instructors, sims, teaching aids, etc. PT 141 rules also allow you to bypass some of the required flight time, meaning less instruction for the same ratings/certificates. Also most 141 schools have better organized programs (ie they follow syllabii, have set lesson plans, and time tables for learning)... some even have standardization manuals that teach their students and pilots to fly using the same techniques and procedures. One advantages of this is that you are being introduced into a "professional" mindset early on in your training.
The down side to PT141 schools is that you often have more BS there as well... additional paperwork, potential scheduling issues, etc. In addition, most PT 141 programs are more expensive (they often carry higher insurance premiums/coverage, and somebody has to pay for the additional resources).
As somebody that attended a PT 141 program (at the University of North Dakota), and taught in both a PT 91 and 141 environment, I can see the benefits of both. However I think that overall, you are better off in a 141 school if you want to follow through and fly professionally.
But that's just my opinion. Like SWAjet mentioned, a lot of it comes down to where you live and what is available in your price range. Do some shopping and visit the schools. Talk with the instructors there (see what the ratio of full time and part time instructors are, how many of them want to move on in their career as opposed to teaching on the side of another job, or being professional CFIs). Also be sure to talk with the students about what they think about the school:
Can they fly when they want, or is the schedule always full?
Are there enough aircraft with the equipment that you want onboard, or are they all poorly equipt and held together with duct tape?
Are they happy with their instructors?
How much time did it take to get particular ratings?
Does the school have examining authority? (Meaning do school employees do the checkrides or do you have to go with an FAA inspector or Designated Examiner?)
Hope that helps... feel free to PM me if you want to chat about it in person, I'm more than willing to offer my insights from my own experiences. ~Josh