As I understand it, the Ahnentafel system was designed for tracking direct ancestors, not for tracking ancestors' decendants. You're trying to use it for both, so that makes things complicated.
I'm not sure what would work best for you, but I checked ancestry.com and they have additional info on numbering systems:
taken from the article "Organizing Your Genealogy"http://www.ancestry.com/learn/library/article.aspx?article=8...
How will you identify or number the individuals you include in your family history? This is an important consideration, since the system you choose provides the means for others to use your research. There are several different numbering systems you can choose from, and the one you select will, again, be influenced by which direction you wish to follow. These are the more common numbering systems:
Ahnentafel — This is an ascendancy numbering system in which the first person is assigned the number 1, his/her father the number 2, his/her mother the number 3, etc. Males (other than the number 1) are always represented by even numbers and females by odd numbers. Double any person's number and you have that person's father; double any person's number and add one and you have that person's mother (3 x 2 = 6 [3's father]; 3 x 2 + 1 = 7 [3's mother]). The advantages of this system are that lineal ancestors are quickly identified by their unique number; it is an easy way to cross-reference information between research files; and it parallels the pedigree chart, the most common tool in genealogical research. The disadvantages of the Ahnentafel system include the difficulty of identifying collateral relatives and the difficulty of following the system if one is uncertain as to relationship to person number 1.
Register — This is a descendancy numbering system developed by the New England Historic Genealogical Society of Boston, Massachusetts, as a method of displaying research in their publication, the New England Historic and Genealogical Register. In this system, the first person in a descendancy study is assigned the number 1. His or her children are then listed in birth order, indented, and identified by lower-case letters (a, b, c, etc.). The children who continue the study are also given an Arabic number, which is written to the left of their birth order letter. Advantages of this system include its ease of use, as it resembles an outline (once a person knows where he fits in the research, he can go in either direction); the ability to trace all descendants of the start person through their unique numbers; and the ability to include vital information, biographical information, and pictures for each individual. Disadvantages of this system include the fact that spouses of the numbered individuals receive no number, excluding them from the study; the fact that children without issue are not assigned a unique number, making it hard to locate them; and the difficulty of adding a previously undiscovered descendant (this can create confusion in the numbering system).
Record — This is a descendancy numbering system developed by the National Genealogical Society for use in its publication, the National Genealogical Society Quarterly, and it offers several improvements over the register system. Most notable of these is that all children in the descendancy families are given a number, whether or not they have issue. Unfortunately, this system suffers from many of the other disadvantages of the register system.
Henry — The Henry system is also a descendancy numbering system, supposedly named for the person who used it in a family history some years ago. The Henry system assigns the number 1 to the individual who starts the line of descent, similar to the previous systems discussed. The difference comes at the second generation, where the oldest child of person number 1 is given the number 11, the second child the number 12, etc. In the third generation, the oldest child of person 11 is assigned the number 111, the second child of that person is 112, etc. Number 12's oldest child is 121, the second child 122, etc. Thus the individual digits represent generations and the specific numbers represent birth order within that generation. The biggest advantage of this system is that each number reveals considerable information about the person, and it is very easy to trace that person's line of ascent back to the individual assigned the number 1. As with the register and record numbering systems, the Henry system does not provide for numbering of spouses, and thus their information is left out of the study. Also, the Henry system can become confusing if there are more than nine children in a particular family, even if one adopts the hexadecimal numbering system (1, 2, 3, 4, 5, 6, 7, 8, 9, A, B, C, etc.).
d'Aboville — This is also a descendancy numbering system named for the person who developed it. This system is identical to the Henry system, except that a period (.) is inserted between generational numbers. Using the examples from the Henry system, the number 1 is assigned to the individual who begins the descendancy. The oldest child of this person is identified by the number 1.1, the second child as 1.2, etc. In the third generation, the oldest child of 1.1 is assigned number 1.1.1, the second child 1.1.2, etc. Number 1.2's oldest child is 1.2.1, the second child 1.2.2, etc. If this last individual had fourteen children, the youngest of these would have the number 126.96.36.199. This modification to the Henry system allows for tracking larger families, but it still does not provide identification numbers for spouses of the children in the study.
Ancestry.com also recommended this:
For more information about numbering systems and how they work, consult Numbering Your Genealogy: Basic Systems, Complex Families, and International Kin by Joan Ferris Curran, Madilyn Coen Crane, and John H. Wray (National Genealogical Society, 2000) and “Organizing and Presenting Family Information,” chapter 8 of Producing a Quality Family History by Patricia Law Hatcher (Ancestry, 1996).