With GM you should begin by creating a
mame.ini file and edit settings in it. This is how you control it.
(to generate the ini you have to use a command line prompt; read here:
http://forum.arcadecontrols.com/index.php/topic,151459.0.html)
There's no short 'quick basic settings for LCD users' written but you should edit the following for a bare minimum providing working lower video and audio lag, I guess...
#
# CORE SWITCHRES OPTIONS
#
monitor lcd
^ mandatory or you'll get an error message
#
# OSD VIDEO OPTIONS
#
video d3d
^ this as I understand actually enables D3D9ex if you have picked one of the patched builds a few members compile and share here with every update
#
# OSD SOUND OPTIONS
#
sound portaudio
audio_latency 1
^ this I think is the minimum you can do to reduce audio latency by default, I don't know much more about it, seems to work a bit for me without issues
(also don't forget to edit the folders paths etc if needed, or put everything 'bios' & 'devices' in the roms folder along with the games roms. For everything picture settings, scaling filtering etc see for yourself. There are ways to further control things using extra .ini files to put in the ini folder, but it is preferable to discuss that in a separate thread or dedicated post)
Your only shader option is HLSL since with GM we're using D3D anyway. You can activate it in the mame.ini as well. It's become tricky to use, there's the usual settings but also a 'raster.ini' file somewhere that's in control of several parameters. Really impractical, and coming with awful default values.
RetroArch works differently using OpenGL and claiming lag/sync acrobatics similar to GM, the difference is that it comes with tons of shaders options configurable via the GUI, it's unbeatable in that area, as even MAME whether using its default HLSL, OGL GLSL, or BGFX doesn't come close in terms of possibilities and convenience.
For everything mentioned above I have no idea:
1. if RA is as capable as GM in terms of lag reduction
2. if using any kind of shaders (HLSL, GLSL, BGFX) adds more or less lag on top of everything or not at all
Lastly; SwitchRes is integrated to GM and turned on by default as it should, I don't think there's any possibility that it would damage your monitor.
I would be more worried about the Intel HD chipset's compatibility and performance, personally when using only that I've seen poorer performance and some things not working properly like for instance the .png overlays