Indeed that is what I am saying. Do the basic novice SS protocol.
Squat, Press, Clean
Squat, Bench, Deadlift
Just focus on adding weight to these 5 lifts and importantly to your body, and you WILL be a lot stronger. Do not waste physical or mental energy with the pull ups yet. They are just an accessory exercise for helping with you main lifts.
If you have had an very easy workout, perhaps if it is the day before your 2 day rest. Throw accessory exercises in at the end.
But really, I would not incorporate them into your regular programming before you have made good progress in the main lifts and feel the additional variety will actually help progression.
I like the the standards Gary gibson mentioned:
1.5xBW squat (reasonably strong, basic target for anyone training the squat)
2xBW squat (decent standard for athletes sports like american football/rugby)
3xBW squat (goal for anyone engaged in barbell sports)
Obviously pull ups are more closeley related to the bench press, but it helps to visualise what is actually important. Also, if you listen to what justin lascek said about the extent of how much you can achieve with the basic programming, yoou will realise its better not to fuck with things too much.
The big lifts & food is important. Nothing else.