Retiring the debt and running for reelection to the Senate
The only donations that can be used to retire the debt from Senator Clinton's 2007-08 primary season race are those made by people who have not already maxxed out to the primary (that is, people who have not yet donated $2300 to Hillary Clinton for President). Money donated for Senator Clinton's reelection to her Senate seat (that is, money donated to Friends of Hillary the official Clinton senate reelection fund) cannot be used to pay down debt incurred by Hillary Clinton for President.
Because right wing groups are likely to target Senator Clinton when she comes up for reelection in 2012 and because a Senate campaign in New York costs at least $20 million to run, Senator Clinton is getting a jump on fundraising for such an effort. If you are maxxed out to Hillary Clinton for President and want to support her reelection to the U.S. Senate, then it makes sense to donate to the Senate campaign fund.
The money raised for the 2008 general election
Assuming (and this remains an assumption, not a given) that Senator Clinton does not become the Democratic Party's nominee in August, under the Federal Election Commission's rules, she can either refund the money to her donors within 60 days after she officially ends her candidacy OR she can get permission from donors to re-designate their general election contributions for use toward Senator Clinton's bid for another federal office - e.g. Senator Clinton may ask people to redesignate their general election contribution to Friends of Senator Clinton to fund her upcoming Senate race. But no money raised for the general election can be used to pay down primary campaign debt.