The basic installation of cables for shifting requires the cable housing MUST be securely fastened at both ends. Make sure there are no sharp bends in the housing. The ends of the sliding inner cable must be attached to the shifter at one end and at the trans at the other. The adjusting takes place on the ends of the housing with the nuts you described. Adjust to take out any play you have.
If the distance shifter moves does not move the arm on the transaxle far enough (or too far) to put the transaxle in gear, you will have to compensate by making the arm either shorter or longer on either the shifter or transaxle shift arm.
Find out how far the arm must move to place the transaxle in gear by removing the cable and shifting by hand, then note how far it needs to move. That rotation will have to be complete to be sure you are in gear. Make sure the cable will move it that far. That applies to the second cable that moves the shaft in and out.
Go step by step and you will get it all to work.
If you are using a Fiero transaxle, you should not have to rework anything. Just adjust the slack out of the cable housing.
RT