Negative sentence of "It seems that~"

In the first

"It doesn't seem that she knows what it means."

the doesn't applies to the seeming. She may well know what it means but it does not look that way to the writer.

In the second;

"It seems that she doesn't know what it means."

The doesn't applies to her understanding. This is generally what is meant by the use of seem to and as such using it in the first way will most often be understood to mean the same as the second way.

Is it okay to use "It seems that + negative form" in written English??

Yes, I think this is the more common use but both will pass the test of understanding.