I'm not writing a series, but I find a detailed timeline quite valuable. I don't use any special program, I just open a new word document (Libre Office) and write a list of the details I need to keep track of. I start with a chapter-by-chapter timeline, with dates and locations.
Chapter Timeline
* Chapter 1--Early March, 1881; Paris Opera (Scene 1: Dressing Room; Scene 2: Onstage)
* Chapter 2--Mid April, 1881; Bordeaux (Scene 1: Chateau; Scene 2: Garden; Scene 3: Carriage)
Etc.
Then I make a personal timeline for the character.
Timeline for MC
1860: Born
1866: 6 years old; Mama dies in childbirth
1872: 12 years old; moves to France
1876: 16 years old; Papa dies
Etc.
If there's a pregnancy or anything similar that needs a detailed timeline, I'll add that as well.
Pregnancy Timeline
Conceived: early October
Near-Miscarriage: early January (@ 3 months)
Reconciliation with Husband: late March (@ 6 months)
Kidnapped: early May (@ 7.5 months)
Rescued: early June (@ 8.5 months)
Due Date: late June (@ 9 months)
Then I create a detailed biography for each main character, and smaller biographies for lesser characters. The biography contains things like: appearance, personality, employment, family members and friends, education, medical information, dress and grooming, personal habits, internal conflicts (such as phobias, confrontations, etc.), speech patterns and mannerisms, likes and dislikes, social ties, personal beliefs, childhood traumas, recent history and backstory, etc. Anything that might be good to know at a later point. I also detail what shifts in characterization occur through the course of the novel. i.e.: What the character is like in the beginning and how they mature and grow as the story progresses.
I've done this timeline/biography combo for several novels now and it's worked beautifully each time.
Also, as far as organization goes, Libre Office and Open Office both allow you to set "bookmarks" so that you click on the menu and automatically jump to whichever bookmark you need. That way, if you have a very long timeline, you can divide it according to year, or chapter, or book, or whatever, and then just click on "Chapter 23" (for example) and jump straight to it, without having to scroll through your entire file. Very useful!