I presume this is the article you used:http://www.arrl.org/files/file/Technology/tis/info/pdf/0004033.pdf
In that case, connect the clip to the top of the matching coil. That particular design
runs the hot lead to the coil tap rather than to the antenna as is done in most cases.
That means that disconnecting the tap disconnects the antenna from the coax.
A few checks you can do:
1) Use an ohmmeter to measure the resistance from the top whip of the antenna
to the car frame. (You may need to extend the leads with some extra wire to do
this.) when the clips are attached to the coils, you should read a low resistance.
Grounding is critical for HF mobile antennas, as KF4ZGZ pointed out.
2) Then measure the resistance to the shell and center conductor of your coax
at the radio end. Both should show a low resistance. When you disconnect the
clip from the matching coil the center conductor should show an open circuit.
3) Answer K5LXP's questions about how the antenna is mounted - that affects
the ground connections as well. For example, a mag mount on a trunk doesn't
provide sufficient ground HF to work well at all, and you can expect to have
problems tuning it.
4) You have an SWR analyzer: set the whip to full length, and the clips on both
coils to the top turns. Tune across the upper HF band and find the frequency
(or frequencies) where the SWR dips, even if the minimum is 3 : 1 or so. Then
move the tap on the loading coil down to the middle of the coil and repeat the
procedure. Keep out of the field of the antenna while doing this - laying on
the ground allows you to use a very short jumper to the SWR analyzer. (If
you can use a jumper less than about 1' long, then looking for the points
where X = 0 may provide useful information.)
Ideally you would check the antenna up to 80 MHz or so: a resonance in the
range of 70 - 75 MHz would suggest a bad connection to the loading coil.