I am assuming that you are not using a cartotank tool. I have not had any trouble filling it. I fill the same as any other cartotank. Slide the carto down to about 1/4 inch past the top lip of the tank(enough to get a needle tip in between the top of the carto and the opening). Slide the needle tip into the gap and fill almost to the top of the carto. Remove the needle-tipped bottle and slide the carto back into place. Make that if you are using a flanged carto that it is oriented properly.
The only issue that I have found is that several (20%) of my Boge cartos do not fit correctly. To remedy this, just turn the tank around, so top is bottom and bottom is top. It seems to fit better that way.