I've never used Book designer, but I haven't noticed any negative impact on books tweaked in calibre as far as displaying them on my 300 or 900.

However, you need to give more information. For example what file type or you converting or modifying and what file type are you converting to. If you a converting from an ePub to a BBeB then you can expect the BBeB to be a much larger file due to embedded fonts and what not, and so a BBeB file will display more slowly on a 300 than its equivelant ePub file.

If you are modifying an ePub to another ePub, you shouldn't see any noticeable difference in display times. However, if you change an ePub font to a font not located on your 300, then it won't display that font but will display the default font instead. As far as I know, the only way to make an ePub display the Georgia font is to add the Georgia font into a fonts directory on the root directory of the 300 and then have the CSS file reference the font file. Search these forums for how to do his.