With the rewrite_indices
which is now in the version on github, you can do
{a, b, c, d, e, f}::Indices(position=fixed).
\eta_{a b}::Metric.
ex:=F_{a}^{b} G_{b c} + F^{b d}G_{d a c b};
rewrite_indices(_, $F_{a b}$, $\eta^{a b}$);
This inserts as many $\eta^{a b}$ (with the right indices) as necessary in order to rewrite the expression using $F_{a b}$ (with lower indices) only.
Note the position of the indices in the rewrite_indices
algorithm: the first argument should give the tensor with the indices in the position in which you want to have them, the second argument is the metric/conversion tensor which you want to use for this. The names of the indices on these two arguments does not matter (just use the right index type).