1: If you are not qualified to fly the aircraft i.e. a complex airplane and you do not have your complex endorsement then you will log it simply as dual recieved not as second in command. There is no such thing as second in command* unless that particular aircraft requires it (it goes more into detail than that, for SEC but that is the basic idea) If you are endorsed for say a complex aircraft and you are logging dual, you may log dual and PIC since you will be the sole manipulator of the controls and are endorsed to legally fly that airplane.
so...total time equals all of your SEL+MEL to include all dual recieved where you were a student pilot and not acting as pilot in command, it is still total time. This applies to SEL and MEL, as a private pilot working on your MEL rating, it will only be dual recieved until you pass your checkride, then further training in a ME, say towards your MEI will be PIC and dual recieved.
2: Not a great thing when you lose your log book but here is what i do. Every so often i make a copy of my most recent log book page for my records, this also applies to anytime i do anything that applies towards a rating such as BFR's and checkrides. Even better is if you can scan your logbook (difficult if you have many thousands of hours) and then keep a scanned copy on a disk. If all is lost you will have to just start a new logbook with the brought forward times that you know for a fact you last had and be ready to do ALOT of explaining when you get to an interview. It happens though, someone suggested to keep old logbooks in a ziploc and put them in the freezer and it is likely to survive emergencies.
I hope this helps...If you want any more detail just ask.
*SEC applies to mostly aircraft over 12,500 such as your lears and your Citation X's, larger King Airs, RJ's and many many more where insurance requires that the aircraft have two pilots. In some cases some of these aircraft can be certified for single pilot operations with possible restrictions. Pretty much all of your GA aircraft will not require 2 pilots though.