This will work:
db.portfolio.insert({
folders: [
{"name":"Folder 1",
"stocks":[
{"name":"stock name",
"id":"stock id1",
"qty":2},
{"name":"stock name",
"id":"stock id2",
"qty":1}
]},
{"name":"Folder 2",
"stocks":[
{"name":"stock name",
"id":"stock id3",
"qty":2},
{"name":"stock name",
"id":"stock id4",
"qty":1}
]}
]})