Not sure if the OP is still monitoring this thread but...
Both Interpretation and Syncopation check boxes affect how you want the notation to show. For the most part syncopation will allow quarter notes to begin on the + of the beat and will also add dots to rhythms that it would normally tie. Such as: 1 e (+ a) written as a 16th then a dotted eighth, versus non-syncopated 16th then a 16th tied to an eighth note.
For the most part I leave interpretation ON as it keeps the vast majority of shorter played notes from showing up as their exact value. Can you imagine what music notation would look like without the staccato indication? Well, turn off interpretation and enjoy...
Finally - one important aspect to making the notation be what you want it is that you MUST quantize the attacks. SUPER IMPORTANT. Else, the lateness or earliness of your attacks will be taken into consideration and added or subtracted to the 'amount' that determines when a note is tied to the next (or dot added).
For example, with interpretation on (and 16ths as the division) I get a note played on the + of beat 1 to appear as two eighths tied when the length value is 0.0.3.0 - but ONLY if the attack of the note was on 188.8.131.52. If I played it early, say 184.108.40.206 (11 ticks early) the length would need to be extended to 0.0.3.11 to make the notation appear the same.
I have done full orchestral scores in Logic (yes, with parts) and while the initial process - the quick and dirty - is great, once you get down to the fine tuning, it can't compete with a real notation program. And as we know, the last 10% is everything! Then again, a real notation program can't do 90% of what Logic can so all is fair I suppose.
So again, Quantize is good for notation consistency.