LVDS Differential Clock input to single-ended output

The first question:

Normally when you have a clock, you mostly have a PLL which generates some other clocks as well. You can easily assign the PLL output clock to an external PLL clock pin (Use your device pin information, there is a dedicated PLL output pin for each PLL). Makes no difference your input clock is single ended or differential.

As far as I know, the ALTIOBUF (ALTIOBUF_in, _out, _bidir) is the same if you need to do it using primitives.

The second question:

No need to connect/reference the negative pin in the design. In Altera, you can simply connect your positive side pin to the PLL if you have already specified that your port is differential (i.e. you have connected the positive side to the positive pin in a differential port and the negative signal on your board to the negative pin in the same differential port). Quartus infers that it is a differential port and uses appropriate logic.