There is a trail that runs from South San Jose to Morgan Hill, I am not sure of the actual trail name but I heard that the trail is not maintained very well and is very prone to multiple flats while riding this trail? Any truth to this? I am considering riding the trail but worried about flatting....

I assume you're talking about the Coyote Creek Park Trail. The Tierra Bella century went through there. No one in my group flatted. The trail, however, is full of slow moving park users. Since it is a public park, they have every right to use the trail. You have to ride real slow to safely share the trail, however. I'll probably take Santa Teresa Road next time.

There is a trail that runs from South San Jose to Morgan Hill, I am not sure of the actual trail name but I heard that the trail is not maintained very well and is very prone to multiple flats while riding this trail? Any truth to this? I am considering riding the trail but worried about flatting....

I've ridden that path many times and never had a flat. How crowded it is depends upon what day and time you're riding on it - Sunday afternoon and there will be others who might slow you down. To me it didn't seem any worse than other MUTs I've ridden on.

There is a trail that runs from South San Jose to Morgan Hill, I am not sure of the actual trail name but I heard that the trail is not maintained very well and is very prone to multiple flats while riding this trail? Any truth to this? I am considering riding the trail but worried about flatting....
As Johnny99 indicated it is the Coyote Creek Trail. It's maintained by the Santa Clara County Parks Dept. It runs 15 miles between Helyer Park and Anderson Park and is paved. I was on it last year and at that time I found it rather well maintained except for some rough areas near Helyer Park. It can get rather windy in the afternoon and it does have a ton weeds that drop those damn little thorn balls. I've gotten a couple flats there, but no more than on the street with glass and other crap. Here's a link that may help.
http://www.parkhere.org/channel/0,4770,chid%253D16482%2526sid%253D12761,00.html

Best,
Frank