Was the Native American population already decimated before settlers and conquistadors arrived in America?
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Let's address the easy issue first. At the time of the Colombian Exchange, the Germ Theory of disease was still about 300 years in the future (and its acceptance more than 400). An educated European of the age most likely would have attributed the natives' susceptibility to Smallpox to their own living conditions, because that's how the prevailing miasma theory worked.
As for the order, it depends a lot on the Conquistador/Explorer/Settlers in question.
For example, Cortes landed in Mexico quite early, and I've been unable to find any reports of disease predating him (doesn't mean it didn't happen, just that I haven't found it). There were however multiple documented plagues that hit the Aztecs after that. There was a smallpox epidemic that swept through their capital right after Cotes' forces were repulsed in 1520 (not so coincidentally, his next attack in 1521 took the city). There was also a salmonella outbreak 20 years later that supposedly killed 80% of the country.
In 1519, when forces led by Spanish conquistador Hernando Cortés arrived in Mexico, the native population was estimated at about 25 million. A century later, after a Spanish victory and a series of epidemics, numbers had plunged to around 1 million.
Plymouth Colony, on the other hand, while quite early by English standards, happened a century later, and that ended up mattering. The settlement was undoubtedly helped a great deal by the fact that they were met by a native who knew English (due to being kidnapped by an English slaver in 1614), and had returned home to discover that in the meantime his entire tribe had been wiped out by a disease.
Thus the English colonists had access to someone who knew their language, the languages of (the surviving) nearby tribes, and how best to farm and hunt the land they had landed in, with nothing much better to do with himself than help them out. And that's of course not even bringing up the fact that the area had conveniently been depopulated of humans like his Patuxet tribe by that disease.
For reference, when Squanto finally did succumb to disease less than 2 years later, his grateful host, colony Governor William Bradford, referred to the cause as an "Indian fever". This seems to indicate that he understood that there were diseases that were killing the natives which the English colonists didn't appear susceptible to. However, it also seems that he was either unaware of, or unwilling to acknowledge, that his people actually were carrying those diseases.
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