No silly questions here. The openings on the clips go towards the back as the metal bar in the soft top hooks into them. As to the talalights I had mine backwards forever and am still not sure which is up or down stock. Someone else will have the answer.
Steve took care of the clip question, no I will take a poke at the lights question.
If I am not mistaken, the brake lights were on the bottom and the turn signals on the top. You can usually tell by the pigtails on the harness - the longer ones go to the top. On the 67s, the turn signals are 2 wire for the turn signals and 3 for the brakes and running lights.
Now, my suggestion is to put the brake lights on top. The roadsters are very low to the ground and the taillights don't look that visible. Putting them on top would increase the visibility. Putting the 3 wire in would not be difficult - just make a Y connector to put on the brake light wire and get some spare 3 wire sockets.
And if you happen to find some super-bright 1157s, it certainly wouldn't hurt to help being seen. Maybe one of those ATV flags on the back bumper...NOT!!
Another option is to find a Pontiac Sunbird convertible in the junk yard and yank off the trunk lid mounted 3rd brake light - or put an LED strip on the Roll bar.