If it is set up correctly the OEM hardtop has its own latches and the softop has its own latches and the softop works perfectly when the hardtop is off the car. My experience is that when you install the hardtop you will get the best and easiest fit if you set the top in place with the latches (front and rear) open, then latch the front, then latch the rear. Also, remember to disconnect the defogger power supply cable from the hardtop when you are removing the hardtop. Its an east thing to forget.

 

the Hardtop uses specific Latches. DO NOT use your soft top latches. The bottom of the latch will say HARDTOP.

Hardtop Latch Hook



The hardtop latch hooks are thicker diameter for the extra weight and rigidity of the Hardtop to keep the hooks from shearing. As well the yoke on the soft top latch is longer, and the hardtop latch mount points are ever so slightly closer to the windshield. Softop latches will leave you with a loose top and wind noise

But yes you can remove the hardtop and use the softtop without issue. If you are wiring in the defroster anf catcher. ensure your car side defroster and hardtop defroster match pins ie both 3 pin or both 2 pin. if one is vice versa you will either need to jump a wire or add a wire. The catcher switch disables the softtop and softtop defrost (if it had soft top defrost 02+)

Likely if you have an 00-03 your defrost side harness is 3 pin, and if you have a hardtop from 04-09 it is a 2 pin defrost. you have to jump the two carside grounds to one pin

Talking about this Junction


Not the 3/4pin junction under the roll hoop behind the driver seat where the subharness connects.

 

 

Soft top will work just fine. Follow what Deckoz said.