it may seem kinda hard to understand at first as it did for me... but try not to understand it... lol. just do it. i dont think there is a better way to do it except to just follow the guide. i actually did everything according to the guide... including calling the mod "my mod." then i changed everything, of course.
but if you want a summary you basically just make a scenario. then go to scenario, and click custom rules. go to scenario properties in the same menu (scenario) and customize your stuff. then theres the unit part. by far the most annoying and confusing. find a unit you want, then download it in a folder, make sure the folder name and the ini file have the same name. make this folder structure. go to civ3/conquests/scenarios. make a folder called "whatever". save your scenario file into the scenarios folder, not the "whatever" folder. then inside the "whatever" folder, make 2 folders, text, and art. inside art, make a folder called units. download all your units into there, but make sure the .flcs and .inis are in individual folders, not just crammed into the units folder. in the text folder, copy the pediaicons.txt and civilopedia.txt from civ3/conquests/text. pediaicons.txt is where you do most of the actual adding. civilopedia.txt is where you make pedia entries, which i omitted because who cares. you do not need to edit civilopedia.txt at all to get your scenario to work. if you dont feel like doing it, dont. anyways. go into the scenario editor, and go to rules, edit. thats where you edit all the crap you want to from units to terrain bonuses and other stuff. go into units, and click add, name your unit (preferably the name of the folder you just downloaded) doing the icon is annoying so i wont talk about it. adjust all the settings of the unit, then, and this is the most important part in the middle, there is a box and on top of the box it says "Civilopedia Entry". type this into that box. PRTO_(unit name) without the parentheses, and make sure instead of spaces, you put _ underscores. look at other units that are in the game to see what flags you should have checked and stuff like that, for example for a cannon unit or for a transport. they can be quite tricky. now go into pediaicons.txt and search for "#ANIMNAME_PRTO_Mobile_SAM" which is the last conquests unit. after that entry, make all your PRTO_ entries. heres the format
#ANIMNAME_PRTO_Mobile_SAM (this is the entry)
Mobile Sam (this is the folder where the flcs and inis are located)
so, for simplicity, it is MUCH easier if everything you use has the same name. for example, if you name the unit something, then make the PRTO_unit_name different, and the folder where its found all have different names, you will get confused very quickly. maybe itd be easier to understand how the program works... the name of the unit that you specify in the editor, is the name of the unit in game. the PRTO_nonsense is what the program looks for in pediaicons.txt. the other PRTO_ crap in pediaicons.txt (#ICON_PRTO_nonsense) is to specificy what icon you see when you consult civilopedia for the new unit. i think its a waste of time and confusing so ignore it. thats basically it...
for the unit icon, if your lazy, use existing unit icons, or you can download corel paint shop pro X2, which reads and edits pcx files, which are the icons.
to do that, find the units_32.pcx file in conquests/art/units. copy that file into your scenario's directory, into the units folder. edit it with that program, and find an appropriate picture of your unit and copy it. then open the units_32.pcx and paste it as transparent into the next blank purple box. (its magenta but whatever). make sure the picture size is 32x32 (pixels). if its not, right click the picture of the unit, and resize it to 32x32(pixels). if the background is already magenta, and its sized correctly, just do regular paste and put it in an empty box somewhere. save it (as units_32.pcx, no alterations!) and then go to scenario, scenario properties and select debug mode from the bottom. then test your scenario by opening the game, going to civ content, and find your mod. play it, select whatever you want, it doesnt matter. if you did it right, you should see the entire map. this is good. its debug mode! yay cheating! anyways. hit Shift+F1 and find your unit (its probably on the very bottom) and hit enter. place the unit. if you see your unit, you win. if not, you did something wrong, or this little summary (which admittedly, is a LOT longer than i thought it would be) is too confusing. most of the problems are just with naming files. look through this thread to find if other people have the same problems. they probably have their solutions.
if you have questions, post them, ill try to get back to you to clarify or whatever, but the real guide is pretty comprehensive. if you specifically dont understand a certain part of it, just ask. i have school and shtuff but ill try to help if i can.