. . . there was just one that continues this day but the main political rules were their puppet rulers.

Do you mean that they were puppets for the main political rulers? ^^;

Its correct that there is only one imperial family (or rather: dynasty), although it's quite extensive at times due to polygamy. Also, during the 13th and 14th century, there was a period when the imperial lineage bifurcated into two competing lineages, which culminated in a de facto split of the imperial court into a Northern and Southern Court for the better part of the 14th century.

Questions about about the Japanese emperor, imperial family, and so on, are quite common: especially the past two or three months had at least four questions on them.

Hence, you might want to browse the FAQ (section Asia - Japan - Politics and Religions - The Emperor and the Shogun), and use the search function (or take a look at some of the threads I linked in my profile, which pretty much collects the more recent ones which actually received answers).