They_____on the program for almost one week before I joined them ,and now we_____on it as

第一个空应该是 spent。sb spend on sth
第二个空就不大清楚了。~

had been working ;are still working

had been working; are still working 考查的是现在完成进行时，用法是：从过去一直持续到现在，并将继续发展下去。