How can I negate time and when to place 在 before time?
I am a bit confused by the 在 in your example sentence, since you don't need it there, 我不在8点起床，我(在?)9点起床。 Frankly, I wouldn't know what this sentence was supposed to mean, if you hadn't provided a translation. If you want to express that something occures at a certain time of the day, e.g. X o'clock, there is no need for 在, just use X点 or X点钟.
As for the proper way:
我不是8点起床，我9点起床。

不是 can be used for such cases, to negate a certain aspect and then to point out the correct aspect immediately afterwards. E.g.
我不是骑车上班，我坐出租车上班。 I do not ride the bicyle to work, I take a taxi.
EDIT:
I can still recall the first time I had learned this 不是 structure and I was confused by it since it sounded odd to me. To get an idea of the difference between 我8点不起床。 and 我不是8点起床。, you have to understand that the first sentence simplay negates the whole statment, while the latter sentence negates only the aspect that is immediately after 不是.
The given translation in this answer is an example of the &quot;是...的&quot; pattern for emphasizing a particular aspect of a phrase. It is not specific to time; for instance:

我不是跟朋友吃晚饭的，我是跟爸爸妈妈吃晚饭的.
I didn't eat with my friends, I ate with my parents.