Ideally you should run the extension upstairs, directly from the line downstairs before the microfilter and have microfilters both upstairs and downstairs.
If you don't want a phone upstairs, you could run the upstairs link from the downstairs ADSL outlet on the microfilter and you wouldn't need to filter upstairs.
for the second option you would need a long RJ11 to run from the downstairs filter to to router upstairs.