Conky cannot be shown above fullscreen by design.
According to the recommendation by freedesktop.org, any focused window at fullscreen has the highest stacking order regardless of desktop environment.
To obtain good interoperability between different Desktop
Environments, the following layered stacking order is recommended,
from the bottom:
windows of type _NET_WM_TYPE_DESKTOP
windows having state _NET_WM_STATE_BELOW
windows not belonging in any other layer
windows of type _NET_WM_TYPE_DOCK (unless they have state _NET_WM_TYPE_BELOW) and windows having state _NET_WM_STATE_ABOVE
focused windows having state _NET_WM_STATE_FULLSCREEN
Windows that are transient for another window should be kept above
The window manager may choose to put some windows in different
stacking positions, for example to allow the user to bring currently a
active window to the top and return it back when the window looses
conky manpage has mentioned some window configuration, which is useful for some desktop environment and to ensure Conky will appear properly on desktop. Any window configuration will work as intended, but will not work against windows at fullscreen.
I don't know what all these commands means but it works (partially).
That will indeed work against maximized windows, but not fullscreen.
The problem is that it is not visible if I am using a pdf in full screen mode, like slides during a presentation.
You will need a tool that features on-screen display (a.k.a. on-screen, or OSD in computing). Conky does not support such feature, and even such named theme is nothing but appearance only.
I'm trying to run it to show a small clock to have time control during the presentation.
There are several tools for such purpose.
impressive: Use this dedicated tool for presentation with a PDF file. The tool has an option to show the current time in seconds or in minutes. The clock will appear at top right of screen, and will be visible within the tool window at fullscreen.
impressive(1) manpage [...]
If this option is enabled, the current time will be shown instead
of the elapsed time if time display is activated with the T key.
Compatible with the -M option.
-M or --minutes
If this option is set, Impressive will show the on-screen timer
(activated with the [T] key) only with 1 minute resolution. By
default, it will show a timer with 1 second resolution.
osdclock: Use this general purpose tool for presentation with any file. The tool has options to customize font, colour, position, and few more. The clock will appear at bottom left of screen, and will be visible above any window at fullscreen.
osdclock(1) manpage [...]
-t locate clock at top left (default: bottom left).
-b locate clock at bottom left (default).
This option specifies the offset from the top or bottom of screen
the text is displayed. The default is 0. Useful to move above or
below panels or applets.
Presentation with clock above fullscreen in action:
TL;DR Conky is designed to appear on desktop and does not support on-screen display. Use a designated tool to show the clock during presentation or above fullscreen.