OK, several questions here. You say, "had to partition my drive in two parts ... for Windows to recognize ...". You ran into a lack of support for "48-bit LBA". Without that you can only make partitions up to 127 GB (by M$ Windows' way of counting). Now, VISTA fully supports 48-bit LBA, so two other ways this could have happened. One is that you originally partitioned and formatted the HDD with an earlier OS, like Win XP original edition or earlier. Win XP added 48-bit LBA support beginning with SP1. The other is that your BIOS may not have supported 48-bit LBA in the on-board HDD controller. If that is the trouble and you have kept your old mobo in the upgrade, you MIGHT be able to download and flash-update your BIOS to enable use of larger HDD's. Or, if you replaced the mobo, almost for sure you have that already, now. Either way you should now have (or can get) 48-bit LBA support in your controller, and it is already in VISTA. So you should be able to re-partition your 250 GB HDD into one volume.
However, in doing that you will surely destroy everything on the HDD. So before starting you would need to back up all your data, etc from the "B" Partition (plus anthing you need from the "A" partition), and test it to be VERY sure it is safely backed up on another device entirely. An external HDD is ideal for this. However you do this, if you can, you are then free to re-arrange the 250 GB drive.
If you have your data all backed up so that you're free to destroy everything on the HDD, you could start by deleting that "B" partition. Go into Start ... Control Panel ... Administrative Tools... Computer Management ... Disk Management. Find that second partition, right-click on it, and chose to delete the partition. You should end up with a disk that has the "A" partition plus a bunch of unallocated space.
Now you're ready to install VISTA fresh. Run the install disk and, when it asks you how to prepare the HDD, tell it to go ahead and wipe out all partitions, then make just one new one with all of the 250 GB in it and install to there. When you're done installing you can copy all your data from the backup to new subdirectories on this C: drive.
However, if you cannot do backups and decide to leave everything on the "B" partition, you can still just install VISTA over top of the old "A" partition. There is some risk that things will go wrong and you'll lose the data anyway, so this is NOT the safe route, and a good tested backup is ALWAYS advised. But if you go this route, as VISTA starts to install it should find the two partitions already existing on your HDD and allow you to install on only one of them (the "A" partition now), leaving the other untouched. That leaves you with two separate partitions as you have now. Some people actually prefer this, anyway. The idea is that, if something really goes bad, you can always re-install VISTA on the OS partition without disturbing any stuff on the other partition.