Gershon - Below you will find what I wrote in the past, in explanation of Tosfos Rosh Hashanah 8a. If you are still confused, we will be happy to explain it in more detail:

(a) It is very helpful to learn Shevilei d'Rakia of Rebbi Yisrael Lipshitz, the author of the commentary Tiferes Yisrael on Mishnayos. It is found in Volume 3 (or Mo'ed 1), before Mishnayos Shabbos. See especially sections 34,35 and also 9, 17 and 31. (The beginning of section 34 is different than Tosfos).

(b) Tosfos then explains when the first Molad occurred, from which every subsequent Molad will be calculated. The Molad occurs every 29 days 12 hours and 793 Chalakim (a Chelek is'1/1080 part of an hour).

Adam was created on the sixth day and was commanded at the beginning of the 9th hour of the day to keep his Mitzvos. Tosfos assumes he immediately saw and sanctified the moon, making it Rosh Chodesh. One cannot see the moon until 6 hours after the Molad, so the Molad must have been 6 hours earlier, or d6 h14 (the 14th hour from the beginning of the night, i.e. the second hour from the beginning of daybreak, on Friday).

However, for the purposes of calculating the Molad, we first extrapolate backwards what the Molad would have been one year before the Tishrei in which the world was created, and this is used as the starting point for calculating the current Molad. Tosfos explains that the reason for this is because the Creation began several days before Rosh Hashanah (Adam was created on Rosh Hashanah), so we add an entire year to our count when counting the number of years since creation (since "part of a year is like a whole year"). This is called 'the year of Tohu.'

(c) To know the day and time at which that earlier Molad would have occurred, we simply subtract for each month 29 days 12 hours and 793 Chalakim. Since we are calculating only the day of the week, and not the day of the month, we can drop the first 28 days (which are divisible by 7), which leaves us (in shorthand notation) 1d 12h 793ch to subtract per month.

According to Rebbi Yehoshua, the original Molad is Nisan of Tohu, and according to Rebbi Eliezer it is Tishrei of Tohu.

We can now calculate the Molad of the Tishrei and Nisan of the year of Tohu. The Molad of Nisan of Tohu was 6 x (1d 12h 793ch) = 9d 4h 438ch earlier than the Molad of Adam's Tishrei (and we drop the first 7 days again, leaving 2d 4h 438ch). This comes out to be d4 h9 ch642 (i.e. the 9th hour of Wed. plus 642 ch).

All the best,

Reuven Weiner