Normally ties go in the opposite direction of note stems. Sometimes this creates a problem because ties cover up notes or other symbols.
To change the direction of ties (to go above or below notes) choose Bar from the Display menu and set the tie direction. You can set the direction for ties in the default, first voice, or second voice individually. Setting Ties only affects ties in the current bar.
If changing the direction of ties does not solve your problems of ties overlapping notes or other symbols, you can change the vertical distance of the tie from the notes it is linking together. Remember that the offset is measured in rows and there are two rows between each staff line or ledger line. Setting Tie Offsets only affects ties in the current bar.