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However a 141 school will teach you to navigate using a VOR and in addition teach you how they work,maybe who created them,how they operate and the history behind them.
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Skymates is both, and the planned difference for my instrument students? With 141 I have to do things in a certiain order. That's about it. If a Part 61 student wants to know how the VOR works, who made it, etc, I'll teach him that, too. I think it's a good thing to know how the VOR works myself.
On the hours thing, 141 is good if you stick with that same school the whole way through. 141 schools are notorious for being finicky about giving credit for previous flight experience b/c it's not part of their approved syllabus if you come in with a moderate amount of time. For example, if you do IR training at a 141 school and have to switch, you MIGHT have to start all over again. Part 61 doesn't really care as long as you meet the FARs. 141 might get you your instrument rating quicker, but you'd have to do 141 again to get lower commercial ratings, otherwise you still need 250 TT. Plus, the airlines don't lower their mins b/c you did 141 over 61. They still want 600 or 1000 or whatever the TT req is.
Personally, I think the 141 stuff is way overblown. You can have a hideous instructor at a 141 school just as easily as you can at an FBO and vice versa with good instructors.