I am fairly certain the answer is yes. that said it is late, so I'll look it up specifically tomorrow.
There is nothing stopping you from using manoeuvres gained from Martial Training to qualify for PoW PrC's.
It looks a little messy to me though, as none of the rules seem to take into account qualifying for PrCs in this way.
Near as I can tell and unless I've missed something:
Martial training manoeuvres and initiator level (etc.) is always tracked separately from initiating classes. A PrC is almost certainly considered an initiating class.
PrCs assume you have a base class to add too, so without one you don't have any previous classes disciplines to add to your disciplines known, nor do you have (for example) any way to recover those manoeuvres in combat (not major issues, but ones that immediately occurred to me, and indicates there may be other, more fundamental, issues).
Your initiator level will be Dragon Fury plus half your levels in other classes.
Ok, so reading up on it, marytial training is indead tracked slightly differently (and seperately from) initiating classes. HOWEVER, it would seem that most of the prestige classes listed in Path of War specifically note that they still grant you maneuvers if you took martial training:
"At every even-number level, an awakened blade gains new maneuvers known from any discipline he previously had access to (either from a martial disciple class or from the Martial Training feat). He must meet a maneuver’s prerequisites to learn it. The character adds his full awakened blade levels to his initiator level to determine his total initiator level and his highest-level maneuvers known."
That said, I need to look and see if the errata made any changes to this.
Edit: errata