I know barely any theory and figured all this out by banging my head against the proverbial wall, keep at it you'll get there eventually.
You can either use trial and error, or count how long the note should be (this is easier for stuff like straight 8th/16th notes).
GP8 can load in an audio file so you can directly compare the note lengths/timing values and adjust from there. I usually do this in eof by importing the tab though as I find the beatmap an easier visual reference. If the sync is off even the correct lengths will sound wrong though so it's a bit of a double edged sword, you really need to get the start offset and the bpm correct from the get go.
If a note needs to be slightly longer/shorter but the next note duration is too long, try using dotted notes, triplets or tied notes (can all be accessed through the note status screen). Rests are also fairly important for getting the durations right and for things to line up properly.
Unfortunately I can't give any really useful advice on this as it's just something you kinda need to figure out and get used to, but if you want something to get you started send the tab over and I can give it a check for ya.