You have to make sure the MIDI is basically very quantized to full steps (1,2,4,8,16,32 notes). That will make your life easier.
You can get into weirder lengths, but they need to be actual musical lengths. If you just sloppily drag lengths around that are somewhere between an 8th and 16th note , you will get weird conversions that are a pain to line up.
Music tools (and 3MLE) have quantizers to help line it all up, though.