I presume you have all your data backed up and only have one hard drive that is partitioned.
Install Windows 7 to the first partition and then later you can expand Windows 7 to cover the space used by the second partition. During the install you will have the option to format using the custom install. Choose the advanced options while selecting the destination drive for partitioning and format options.
Please note that if you use Windows 7 install to remove and create partitions, there will be a small 100MB partition created for the boot files. Personally I don't want the 100Mb partition created and choose to only format the existing partitions.
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