Help me understand reading analysis

1. Self analysis differs from analysis, only in that it allows me to make notations. Is this correct?

2. If the self analysis box is checked, then it only shows the lines. (I have mine currently set at 3, and yes I can change that.) My question arises when the self analysis box is not checked but the show lines is. Directly under those check boxes, it shows on my screen Nc3 is a book move. Under that (where I am currently at) it shows 5 full moves starting with the 3rd move, 3. Bb5 d6 4. 0-0 etc. Directly to the right of all of that is a white rectangular box with the numbers + 0.25 in it. (white has slight advantage). Then below all of this, is the 3 lines I am running which consist of various lengths of full moves. However the very first 5 full moves of the first line exactly matches the line of 5 moves under the check boxes, but it has 9 more moves added to it. Beginning of the first of three lines (which has the matching moves) is a white rectangular box with the numbers +0.53. Why do these numbers not match? At first I thought it was because the greater depth.

3.  Nc3 d6 4. Bc4 Nf6 5. O-O e6 6. d4 cxd4 7. Nxd4 Be7    +0.25

3.  Nc3 d6 4. Bc4 Nf6 5. O-O e6 6. d4 cxd4 7. Nxd4 Be7 8. Be3 O-O 9. h3 h6 10. Bb3 Na5 11. f4 d5 12. e5 Ne4 13. Nxe4 Nxb3 14. Nxb3 dxe4 15. Qxd8 Rxd8  +0.53

 3... d6 4. O-O Bd7 5. d4 cxd4 6. Nxd4 Nf6 7. Nc3 e6 8. Nxc6 +0.20

 3... d6 4. O-O Bd7 5. d4 cxd4 6. Nxd4 Nf6 7. Nc3 e6 8. Nxc6 bxc6 9. Be2 Be7 10. Qd3 O-O 11. Qg3 Kh8 12. f4 e5 13. fxe5 dxe5 14. Qxe5 a6 15. Qg3 Kg8 +0.48

 4. Nc3 Nge7 5. d4 cxd4 6. Nxd4 a6 7. Be2 d5 8. Nxc6 bxc6 +0.30

 4. Nc3 Nge7 5. d4 cxd4 6. Nxd4 a6 7. Be2 d5 8. Nxc6 bxc6 9. O-O e5 10. Na4 Ng6 11. exd5 cxd5 12. c4 d4  +0,67

How should I be interpreting these numbers and which one should I be paying attention to?

Good question. I have often wondered what the function of the "self-analysis" button is.

You seem to be using the "Show lines" to provide analysis of openings, which is a particularly difficult task for engines. There are so many branches and permutations possible. 

According to Martin Stahl, "Self Analysis turns off the move evaluation such as book move, blunder, inaccuracy. When I use it the option I also will turn off the lines option as well for a true self analysis."

"Self-analysis" doesn't seem to be addressed on the Help page article about the analysis function. https://support.chess.com/article/365-how-do-i-use-game-analysis

Good point about using the self analysis but unchecking the show lines. Thanks for the link but I had already seen that. I am still very confused on the difference of numbers between the lines since they are the same moves. If it is because of the in depth reading changing them, then it seems rather pointless having the first line only carried out 5 moves. Rather the whole point of seeing what the computer claims to be better moves. Yes I am using the computer analysis on my last finished game to see better choices that I should have made.

Thanks