I know in the Free, Skaters usually put their transitions in the choreographic sequence and Yuzuru puts his transitions during the step sequences, Can a skater do multiple transitions on either sequences or it only depends on their stamina?
Your question is unclear; you might be misunderstanding what transitions, step sequences, and choreo sequences actually are.
Step sequence: A series of turns and steps (twizzles, brackets, loops, counters, rockers, choctaws, etc) that covers the entire rink, either in a straight line down the length of it or in a circle/oval around it. The skater must do several of these complex turns/steps with their feet, and a step sequence usually lasts about 20-30 seconds. A step sequence is a required element and is listed on a skater’s protocol as StSq. It has 4 levels and can receive positive or negative GOE.
Choreographic sequence: A part of the program where skaters may include various different moves, as long as it covers the entire rink. Skaters can do turns/steps, like in a step sequence, mixed with moves such as spreadeagles, ina bauers, spirals, split jumps, hydroblades, cantilevers, etc. A choreo sequence (ChSq) is a required element in senior singles’ free skates, has 1 level, and is evaluated on GOE.
Transitions: A category of Program Components evaluating the difficulty and quality of connecting steps/turns and other moves between elements. Transitions are NOT an element on their own, like step sequences and choreo sequences are, though they may share many of the same steps/moves. Javier doing a layback ina bauer into a 3Lo is considered a transition. Yuzuru doing a layback ina bauer in his choreo sequence is not considered a transition, it’s just part of his choreo sequence. Transitions are brief and scattered around a program, often as the entries and exits to elements such as jumps and spins.
Hope that clears things up!