You can use "Input manual offset" to make sure your tracks sync up properly.
You need to do a "Loopback" test and find out exactly how many samples your files are being offset by then put that number in the box.
You do the test by plugging a lead from the output of your soundcard back to the input and then recording something with a sharp peak(eg. snare drum, click, etc) back into REAPER. You then need to check the difference in samples between the original peak and the recorded one, this is your offset.
[IMG]http://img115.**************/img115/6237/beforewq2.png[/IMG]
You can see the gap, you just need to count the samples in between the peaks and put it in the "Input manual offset" box.
An easy way to count the samples is to draw a loop selection from peak-to-peak and it will display it in the loop length in the transport.
With "Input manual offset" properly set....
[IMG]http://img402.**************/img402/7858/afterga9.png[/IMG]
The offset
may change if you change your asio buffer size, so have a look at what your offset is at the ones you use.
It would be cool if REAPER had a built-in project with a guide for adjusting this.