The value that can be entered into the Max Loaded File Size box depends on your computer, the larger the number the more memory is used. This value can vary the time to complete the map. Start with the default value of 10 and experiment with different amounts.
The Number Of Colours value affects the size of the finished map, compression is improved with a smaller number but the image quality will reduce if the value is below 48.
The next step is to specify a path to your maps by clicking on the ADD button in the Source Maps page, and then you can browse to your map folder and click OK.
The program will scan all maps in the selected folder and create thumbnails. This could take several minutes depending on how many map files are in the folder. The thumbnails are automatically saved for future use and will be quicker to load next time
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The next picture shows the loaded images and some details. You will notice in the left upper window there are two paths, only the map thumbnails of the path that is checked is displayed. Check or uncheck the desired paths, more paths can be added by clicking the ADD button. Make sure the Show Map Outlines box is checked and if you wish to view the map names check the Show Map Names box.
In the right hand pane the loaded map thumbnails are displayed. The blue border around each map indicates it is selected. The lower left window lists all map files in the selected path and the boxes are checked if the map is selected. Map files can be selected or unselected by clicking on the Select Map button 
and then double clicking on the map thumbnail, or alternately clicking on the check box. When selecting your maps be aware that this program
“squares off” the finished map so as in the case of the above map selections the finished map will consist of all the blank space in the area north of Esperance and east of Lancelin and will create a very large map taking much longer to create. It may be better to make more than one map of the area so there is no blank areas.
Pay attention to the pixel scale column and note the largest value of the selected maps as this value must be entered in the Map Scale box in the Destination Map page. This value is the metres per pixel scale of the finished map and I have found that if this value matches the highest scale of the original maps the finished map will display the same as the originals.
Select the Map Datum and Map Projection if desired.
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You are now ready to merge your maps.
From the Source Maps page click on the Create Map button and click on From Selected Maps which opens the Save As box. Enter a name and browse for the desired folder and click OK.
The Generating Map Box now appears until the map is finished. You can estimate the time it will take to make the map by watching the Row values at the bottom left corner of the Generating Map Box. Time how long it takes the Row number to increment in .jpg)
seconds then divide the large Row value by this time and multiply it by 120. The result will be the approximate amount of hours the map will take.