Generate certain list from two lists

Yes you can use MapThread:

l3 = Join @@ MapThread[Function[{x, y}, Insert[x, #, 3] & /@ y], {l1, l2}]

Here's a more esoteric version that builds lists of mapping operators from l2 and then applies them to the elements of l1:

l3 = Join @@ MapThread[Through[#1[#2]] &, {Map[Insert[#, 3] &, l2, {2}], l1}]

See here for a discussion of the Through[#1[#2]]& operator.

You can also MapThread the function Thread[Insert[#, #2, 3]] & on the pair of lists {l1,l2}:

Join @@ MapThread[Thread[Insert[#, #2, 3]] &, {l1, l2}]

{{Mn, Mn1, {1, 1, 0.}, 1., B, 1.4}, {Mn, Mn1, {11, 11, 0.}, 1., B, 1.4},
{Al, Al1, {2, 2, 0.}, 1., B, 1.4}, {Al, Al1, {22, 22, 0.}, 1., B, 1.4}, {Al, Al1, {222, 222, 0.}, 1., B, 1.4}}

Alternatively, use the MapThread/Thread combination to create pairings appended with 3 and apply Insert to the resulting triples:

Join @@ Apply[Insert, 
  MapThread[Thread[{##, 3}, List, {2}] &, {l1, l2}], 
 {2}]

same result