In the Reaper's belly
In someone else (explain)
This causes some real confusion on what's going on. In the only fight we see using the Shiki Fuujin (Reaper Death Seal) the seal appears on the users stomach. And that seal appears to be an exact match for the seal on Naruto's stomach.
So basically we are left with a mishmash of contradictory information.
Supposedly the yang chakra is in Naruto, but wasn't sealed with Shiki Fuujin.. Naruto has an apparent Shiki Fuujin seal on his stomach, but he isn't the one that used technique and supposedly that technique wasn't used to seal the chakra in him..
Minato's body should have that seal on it. And the yin chakra should be with him in the seal (in the reapers belly).. Jiraiya was most likely either wrong, or mistranslated on those pages.. Possibly Kishi just screwed up.. So we don't really know what happened.
Here's an idea: the entirety of the Kyuubi is sealed within Naruto, but when the seal is functioning properly it only allows him to access the Yang Chakra.
There is no doubt that the 4th was able to combin this jutsu with other sealing jutsu (for example the host system introduced by the legendary sage)
We can only speculate on this part however it seems the most logical to me.