MultiHexTutorial
(quickly written, I'll explain it more in detail when I have more time -- Ayin)
First example: mountains
Suppose we have the following map to fill with mountain tiles:
And we have the following images to fill it:
- tile1: 

 - tile2: 

 - tile5: 

 
We will use the following three rules to fill the mountains. Beware: Spaces into maps do matter!
[terrain_graphics]
        map="
.  ,  1
,  .
.  ,  1
,  .
.  ,  1
,  1
1"
        [tile]
                pos=1
                type=Mm
        [/tile]
        probability=30
        no_flag="base"
        set_flag="base"
        [image]
                layer=-1000
                name=tile5
        [/image]
[/terrain_graphics]
[terrain_graphics]
        map="
.
,  1
1"
        [tile]
                pos=1
                type=Mm
        [/tile]
        probability=30
        no_flag="base"
        set_flag="base"
        [image]
                layer=-1000
                name=tile2
        [/image]
[/terrain_graphics]
[terrain_graphics]
        [tile]
                x=0
                y=0
                type=Mm
        [/tile]
        probability=100
        no_flag="base"
        set_flag="base"
        [image]
                layer=-1000
                name=tile1
        [/image]
[/terrain_graphics]
The first rule, regarding the biggest mountains, will apply first. It will include, with 30% probability, the big 5-tile mountain range. This will make, for example, something like this.
The second rule will then apply. Note that the previous rule had set the "built-m" flag, thus preventing the mountains from the second rule to overlap the place where the first mountains already have been placed. The result will be something like that:
The, the last rule, with 100% probability (the probability key could have been omitted) will apply. It will place a mountain tile on the places where no other mountain tile was placed. The final mountain range will look like that:
Village with a tower
To add a building with a tower that spans over 2 hexes, you may use the following rule (Tt being the character representing the building hex)
[terrain_graphics]
     map="*, 1"
     [tile]
         pos=1
         type=Tt
     [/tile]
     [image]
         name=tower # a 36x72 image
         position=vertical
         base=36,108
     [/image]
[/terrain_graphics]
Reference
Map:
'.' means "this rule does not apply to this hex" (i.e: no image will be set to this hex, this hex will not be checked for flags, etc).
'*' means "this rule applies to this hex, but this hex can be any terrain type".
Flags:
no_flag="built-m" means that the rule only matches if the flag "built-m" is not set.
set_flag="built-m" means that the rule, upon matching, sets the flag "built-m".