Transcribing by ear

Hi there, I'm trying to transcribe a song via musescore. It is quite easy to determine the key and the pitches of the notes of the song as I'm well acquinted with the notes on the instrument. It is worth mentioning that I'm using a small chromatic tuner to double check my pitches. I have written quite a number of bars already pitches are fine, but not note durations. When I listen to the music and play the notes it sounds correct. However if I let musescore play the notes the note duration/value seems to be incorrect. I used a metronome to check the speed and set it on musescore. I tried to tie notes across measures which helps a bit, but some notes seem not visible. For example if the song is in 4/4 I end up with say three note values in total in a measure and the program is not allowing me to alter this. Additionally I'm low brass and keen to complete the song for treble clef players as well. I intend to use the chromatic tuner, fingering chart for the small trumpets. I can play alto notes on the trombone, but soprano would be a bit high for me, could anybody suggest an easier way for this as well. This is my first transcription using musescore and I need to understand what I am possibly doing wrong as I want to play with other band members and not just tenor.