The way to get the icons to appear in the city screen is as follows:
In the directory CivIII\....\Scenarios\Your_Scenario\Art\City Screen\ are two files: buildings_large.pcs and buildings_small.pcx.
1. You must add the corresponding small icons to these files.
2. Take note of what building's Icon is above where you put the new icon, and open the Civilopedia.txt file located in the ......\Your_Scenario\Text\ directory.
3. Search for the building whose Icon is in the row above your new building. When you find the entry, it should read something like this:
{Example:}
#ICON_BLDG_Temple
Culture
8
\art\civilopedia\icons\buildings\templenalarge.pcx
the number on the third line is the row number for the Buildings_large and Buildings_small.pcx files.
4. Increment this number by 1 (since your building's icon is on the row immediatley under this building), and when you add your own pediaicons entry, use that number for the row:
{Example:}
#ICON_BLDG_Crypt
Single
9
\art\civilopedia\icons\buildings\cryptlarge.pcx
\art\civilopedia\icons\buildings\cryptsmall.pcx
If you follow all 4 steps, it should work properly.