I am not sure how STAAD deals with the specifications of the unsupported length for top flange compression.

For example, if I have a truss whose top chord is laterally supported at every other node (i.e. two member lengths being unsupported), then should I highlight every two members (of the top chord) seperately and then tell the program to take their combined length as being unsupported, or should I highlight the entire top chord and then specify the correct unsupported length.

The value you specify for UNL is what STAAD uses for the expression Lb which you will find in Chapter F of the AISC ASD & LRFD codes. Starting from Version 2001, UNL has been replaced with UNT and UNB for these codes. If the Lb value for the top flange is different from that for the bottom flange, you have to specify the corresponding values for UNT & UNB.

So if the bracing points are at every alternate node, first determine the distance between the alternate nodes. Then assign that value for both beams which exist between those nodes.

For example, if you have

Member 5 connected between nodes 10 and 11, and is 6.5 ft long
Member 6 connected between nodes 11 and 12, and is 7.3 ft long

and both the top and bottom flanges are braced at nodes 10 & 12, you can assign

UNIT FEET
PARAMETER
CODE AISC
UNT 13.8 MEMB 5 6
UNB 13.8 MEMB 5 6

To assign these parameters using the GUI, while in the Modelling mode, select the Design page from the left side of the screen. Make sure the focus is on the Steel sub-page. On the right side, select the proper code name from the list box on the top. Click on the Define Parameters button along the bottom right side. In the dialog box which comes up, select the tab for UNT and UNB, specify the value, and assign it to the appropriate members.