This is how I've gotten Clementine to work on the steam deck. The steam deck was my first Linux machine so I was a total noob at it all, still am.
I'm going to assume you have the same amount of Linux exp i did when i started. (so none lol)
Your steam deck boots up in Gaming Mode. Hold down the power button and a menu will come up and click "Switch to Desktop Mode".
To head back to gaming mode there is a icon on the top left of the desktop, do not hold the power button down while in desktop mode.
First you need to copy over the PSU install files and the patch and get it unzipped. I had trouble with this so I unzipped this on my PC and put it on an SD card and copied it to my steam deck.
While in desktop mode open Stream> Add a Non-Steam Game to your Library > Select the installer
Then Settings on that game > Compatibility > Proton 7.0.4
also name the shortcut ClemPSU (i recommend)
afterward, go ahead and hit PLAY which should open the installer then feel free to install
Once its done installing, Settings > Change the target to PSUC.exe and the target folder
*You must change the target and not just add PSCU.exe as a new steam game*
from there you should be able to get the game open in Gaming Mode only
It will patch and then odds are you'll be stuck on "Patch file has been saved. Press any button to exit" or whatever it says
you'll need to bind Enter to an input (like one of the four back buttons)
go back to Desktop Mode, delete PSUC.exe and rename PSCU.exe.patch to PSUC.exe.
now you will need to edit the ini file to change your settings because i could never get the launcher to work.
head to Home > .steam> steam > steamapps >compdata >(10 digit number) > pfx > drive_c > users > steamuser > AppData > Local > SEGA > PHANTASY STAR UNIVERSE
I know its alot but you only do it once.
match your settings with mine below. One downside is that you will lose one keybind. I sacrificed first person zoom but you can still add it later by binding Q to a button on your deck. you will see.
make sure to save when you are done.
[system]
VER=10100
PASSWORD=1
SERVERSAVE=0
CHATLOG=1
LANGUAGE=AE
MOUSE_OPERATION=0
[path]
MEDIA_PATH=DATA\
LOG_PATH=LOG\
BACKUP_PATH=BACKUP\
MOVIE_PATH=DATA\
SCREENSHOT_PATH=SCREENSHOT\
[screen]
RESOLUTION=5
WINDOW_MODE=0
COLOR_MODE=1
VSYNCWAIT=0
WORDWRAP=1
[performance]
INT=1
RATE=2
LOW_TEX=2
CLIPPING_SCENE=0
CLIPPING_OBJECT=0
CLIPPING_ENEMY=0
CLIPPING_PLAYER=0
CALC_MOTION=0
POST_EFFECT=0
LOD0=12
LOD1=15
LODBUF=38
MIPMAP=1
ANISOTROPIC_FILTER=0
SHADOW_LEVEL=0
[sound]
BGM=1
SE=1
STICKY_FOCUS=1
BUFFER_TYPE=DEFAULT
[keyboard]
WND_MM_SC1=F1
WND_MM_OPEN=HOME
PL_MOVE_F=W
PL_MOVE_B=S
PL_MOVE_L=A
PL_MOVE_R=D
PL_ATK_A=DOWN
PL_ATK_B=RIGHT
PL_PALETTE0=UP
WND_AP_CP=E
PL_CAM_BACK=LEFT
PL_SBJ=Q
WND_CONVERT=SPACE
PL_VEHICLE_ACC=RIGHT
WND_MM_SC2=F2
WND_MM_SC3=F3
WND_MM_SC4=F4
WND_MM_SC5=F5
WND_MM_SC6=F6
WND_MM_SC7=F7
WND_CS_UP=I
WND_CS_DOWN=K
WND_CS_DECIDE=L
WND_CS_CANCEL=J
SND_MOVE_U=UP
SND_MOVE_D=DOWN
SND_MOVE_L=LEFT
SND_MOVE_R=RIGHT
WND_SORT=M
ML_ANS=Z
[gamepad1]
BUTTON_B=1
BUTTON_A=2
BUTTON_X=3
BUTTON_Y=4
BUTTON_L1=5
BUTTON_R1=6
BUTTON_L2=10
BUTTON_R2=9
BUTTON_R3=11
BUTTON_START=8
BUTTON_L3=7
BUTTON_U=0
BUTTON_R=0
BUTTON_D=0
BUTTON_L=0
STICK2_INPUT_X=4
STICK2_INPUT_Y=5
[clementine]
RES_WIDTH=1280
RES_HEIGHT=800
MAP_POS_X=0.755
MAP_POS_Y=-0.685
MAP_SCALAR_X=0.6
MAP_SCALAR_Y=0.6
RES_MOD=False
RENDER_MOD=False
QS_MOD=False
NOVID_MOD=False
Now head back to gaming mode and launch the game. head to the controller layouts. you may see a saved one on community layouts name "Broccoli layout PSU" if not ive attached screenshots for you to mimic.
https://imgur.com/a/iqK4WLN
The layout may seem weird and you can tweak it anyway you want. i like the F keys on the back paddles to armor swap quickly and i use the other F keys to quickly use trimates and star atomizers.
Feel free to DM me on discord or post here if you have any issues or things that can improve this process.