Hi Annette,
What time of year are you going? Are the date(s) you want sold out and offer only tours?
Normally, you can purchase your ticket(s) without a tour. The Sistine Chapel visit is included. Keep in mind about the dress code for women, men and children -- shoulders and knees covered. Also, no big bags or large umbrellas -- they will most likely have to be checked.
My first visit to Rome, I took a Vatican tour. After the Sistine Chapel visit, the guide left us on the terrace entrance to St. Peter's. We didn't have to go through security again. But, there can be guards at the doors' entrance to St. Peter's. My ticket included St. Peter's. But, there is no entrance fee to the Basilica anyway. (With the guide, the Vatican ticket allowed us who wanted to go, to by pass the security line below.)
And, if you decide to revisit St. Peter's Basilica, you won't need a ticket. There is a security line, and it can be long, depending. Removal of jackets, hats, bags is required to be put on moving belt to be scanned. I went a number of times, and one time, I saw a guard ask a man to remove his belt.
Bottled water was allowed but had to be put in your bag. No food walking around.
On the ground level near the steps leading up to St. Peter's, there is entrance to storage cubbies and restroom facilities. Even though it may be "manned," I would not leave anything of great value. If you can bring a small to medium size tote/bag/backpack, you should be okay.
No charge for restroom. I don't know about the storage area.
I absolutely fell in love with St. Peter's. I went a few times and never tired of it. I also got a nice surprise one day which really made that visit all the more special. I went in December (both trips to Rome.)