@Zelbinian it seems to me that you are conflating two types of representation in your question.
If you are making an Isotype chart, then each pictogram represents a certain number of things. In order to create a higher value, you simply add more pictograms. There are no scaled x or y axes. Because the pictograms are typically arranged in rows, the the width of an icon is the measure you need to be concerned about. If you need to represent a fractional measure, you can simply divide the width of the pictogram.
A starting point for Isotype: http://en.wikipedia.org/wiki/Isotype_(picture_language)
If you are making a bar graph, or a stacked bar graph, then the length of the bar (or height of the column) when compared to a scale on an axis indicates the specific value. The overall extent of a bar when compared to others gives the reader a quick but rough indication of relative measure.
You can declare a pictogram to be of a certain value. Say you were representing how many thousands of tonnes of goods are shipped by truck in a year. You could make a truck icon make a legend: 1 truck pictogram = 1000 tonnes. If you had 12,000 tonnes you'd show 12 trucks. 12,250 tonnes would be 12 and quarter trucks.
You can divide your pictogram into fractional units by: drawing a rectangle over the pictogram matching its width. In Illustrator set the reference point to middle left. With the rectangle selected, use the width value box and input math such as 1*0.4 for 40% and hit Return (Enter). Select both your pictogram and rectangle and then go Object > Clipping Mask > Make (⌘7 on a Mac). If you want a Pictogram to represent 40% of one thing and 60% of another then make another the same way but from the opposite side and then align their edges.
It may be that you don't want to do an Isotype chart or it's not suited to the information you need to express. In that case it's far better to make a simple and clear bar graph. I strongly recommend not trying to map pictograms onto the bar (or columns) because Isotype just isn't for that. Instead go for accuracy and clarity in the information. Locate extra labels atop the columns or at the end of the bars to indicate precise measures, especially if the scales are far away and make it hard to compare. If you want visual interest rely on colour, contrast and size rather than decorations that don't add meaning.
I would illustrate all this but I really need to sleep. I will check back in tomorrow sometime or on Friday.