Spain seemed content with French ambitions and were a valuable ally, especially when there were Naval powers such as Britain threatening both of them. Why did Napoleon not make more of an effort to stay at peace with them, while he was trying to invade Russia as well. It seems to be a pretty big mistake for someone of his apparent genius.
Were Spain close to breaking away or did Napoleon just decide to invade them?
A few apologies to start. First to my delay, it took me some time to write this massive message and I haven’t had enough free time. Second, to my ignorance on Napoleon; this is why I decided to base my answer on the Spanish side of this event. Third, to my lengthy explanation; I thought that to properly understand the motivations of Napoleon in 1808 we needed to understand the Spanish political situation, which couldn’t be understood without going back to the war of 1793-95, which couldn’t be understood without going all the way back to the beginning of the French Revolution in 1789. That’s why I wish I can summarise it in a TL;DR.
TL;DR
Napoleon felt he couldn’t trust Charles IV and his minister Godoy because of their independent interests and incompetence, so he decided he would occupy Spain and force Charles IV to break apart Spain and make it a vassal state. But Prince Ferdinand messed all his plans when he staged a coup against his father and Godoy, and crowned himself King. Napoleon couldn’t allow a younger, more popular, more capricious and harder to control version of Charles IV to stay in power. He also couldn’t restore the unpopular Charles into power. So he forced both to come to him, arrested them and gave the Spanish throne to his brother Joseph to try to keep control of Spain. The move backfired terribly, and this was the beginning of the “Spanish Ulcer”.
In the following comments, the full answer.