Switch – meaning of 1GE/5GE SFP in Cisco Switches

Dedicate uplink ports are an anarchism from when MDI/MDI-X was not detected and account for by the switch software. In some cases you had a physical switch you needed to flip on the switch to turn it on or off.

That said, I don't think i've seen a switch that didn't have auto MDI/MDI-X capabilities (or it was controllable in software ) in about 8 years. You should be able to connect you workstation to an "Uplink" port and it'll work just fine. You may have to make software configuration adjustments in the switch config, you documentation should tell you if you need to and how to do it.

GigE will run fine over Cat6 up to 100 meters (and, in most cases, Cat5e as well). In general, you would need to use fiber SFP modules if:

1. Your cable run exceeds the maximum length for the cable type.
2. Your cable run will be close to a significant EMI source (though this can be mitigated with shielded cable).
3. The endpoints have different electrical grounding (e.g. different buildings).

Inside the rack, I see no reason to use SFP+fiber between the two switches unless you're completely out of 10/100/1000 ports and you can't vacate any. Even in that case, I'd suggest using 1000base-T SFP modules, since a Cat6 patch cord will likely be cheaper and more readily available than a fiber one.

Going between floors, you need to be aware of items 1 and 2, above. Item 3 probably doesn't apply, but it would be a good idea to verify with an electrician just in case.