Generally you just run the router wifi antenna vertically polarized. The
alfa dongles have a "knuckle" in the antenna so you can change the
pitch. There is no reason to rotate a vertical antenna since they are
omnidirectional, but you might use the Alfa clipped to the back of a
notebook or use it flat on a table, so the antenna itself needs to be
adjusted to be vertical.
I'm not really sure why you are agonizing yourself over this. The alfa
is about as cheap as it gets unless you want to go with mystery stuff on
ebay.
You can't fight physics. Generally more is more and space is better than
being confined. The larger antenna works better and having it in free
air is better than embedded in a notebook. The Alfa devices are good for
war driving.
The only thing I've noticed is the 5.8GHZ/2.4GHZ version is not as
sensitive as 2.4GHz all by itself. If you have interference issues, then
I suppose 5.8GHz is a good choice, but the 2.4GHz dongle has far better
reception.
Since you say PC rather than notebook, it wouldn't hurt to explain what
you are trying to achieve.
If for any reason you are going to change the antenna, I'd go with the
Tube-U version. It is far more rugged and comes with a N-connector
rather than RP-SMA. The good antennas will use N connectors.