'... when buying my [unspecified] mac [model] ...' - specific Macintosh models do not support accessing greater than (approximately) 128 GB of storage space.
Download
Mactracker and view the specifications for your (unspecified) Macintosh model. Click on the respective windows' 'Expansion/Port' tab, and look for the 'Large Drive Support:' line.
If 'No (Maximum of 128 GB per drive)' is listed - you could:
01. Leave the 250 GB as is - formatted at 128 GB.
02. Purchase and install a
PCI to ATA card capable of supporting hard disk drives, hdds, greater than 128 GB.
03. Remove the 250 GB hdd and place it into an external
FireWire case.
If a PCI to ATA card is installed, and the 250 GB hdd is connected, or the 250 GB hdd is installed into an external FireWire case - reformat the hdd and all 250 GB (actually approximately 230 GB) will then be accessible.
If the 40 GB hdd is your boot drive, consider purchasing a Western Digital or Seagate 120 GB hdd as its replacement. This way you will have a great deal of space for MacOS X to use, in addition to any additional software you will install.
If your unspecified Macintosh model has a Zip drive bay, you can also install a 3.5" hdd into it, as well.