1. An aliya must be at least 3 pesukim
2. An aliya cannot start less then 3 pesukim from the beginning of a parsha lest someone walk in and mistakenly think that the previous aliya was only the 1 or 2 pesukim at the beginning of the parsha
3. An aliya cannot end with less then 3 pesukim left in the parsha lest someone leave and think that the next aliya will only be 1 or 2 pesukim (to finish the parsha).
There is no way to split up the Rosh Chodesh laining as is without violating one of these principles. The Gemara brings up a similar problem by maamados and answers that you repeat one of the pesukim. The maskana of the gemara is that we repeat a pasuk in the middle. It is not so clear what the maskana really means (is it referring to Rosh Chodesh or maamados? What does middle mean when you have 4 aliyos?).
The Ran quoting the Geonim explains the maskana as referring to Rosh Chodesh, and the laining is as follows.
Kohen - the first 3 pesukim
Levi - repeat pasuk 3 and read the next 2 (pesukim 3,4,5)
Shlishi - read pesukim 6,7,8 and the 2 pesukim of the parsha of shabbos
Revii - read the parsha of Rosh Chodesh (5 pesukim)
The Ramban asks a bomb question. What does it help that we repeat pasuk 3, we are still violating principle 2. By starting Levi with the third pasuk someone who walks in may think that the first aliya was only 2 pesukim, so what did we gain by repeating. Therefore, the Ramban says that the maskana of the gemara was for maamados and on Rosh Chodesh you don't repeat anything (and violate principle 2).
In Shulchan Aruch (Siman 422) we pasken like the Geonim quoted by the Ran.
The Gra there based on a Maseches Sofrim comes up with a way to split up the aliyas by repeating
Kohen - the first 3 pesukim
Levi - next 5 pesukim (4,5,6,7,8) until the end of the parsha
Shlishi - repeat pesukim 6,7,8 and the 2 pesukim of the parsha of shabbos
Revii - read the parsha of Rosh Chodesh (5 pesukim)
What the Gra proposes is an elegant solution to the problem and it is interesting that the minhag haolam is not like the Gra. In Israel many of the shuls (for example where I daven) are noheg like the Gra.