Hi there,
Your CRT should display the same resolution as original hardware would, if you're using the analog port.
For instance, Castlevania on the Mega Drive switches between 256x224 and 320x224 and that's exactly what the MiSTer will display. Your ini-file should look similar to this:
[MiSTer]
key_menu_as_rgui=0 ; set to 1 to make the MENU key map to RGUI in Minimig (e.g. for Right Amiga)
forced_scandoubler=0 ; set to 1 to run scandoubler on VGA output always (depends on core).
ypbpr=0 ; set to 1 for YPbPr on VGA output.
composite_sync=1 ; set to 1 for composite sync on HSync signal of VGA output.
vga_scaler=0 ; set to 1 to connect VGA to scaler output.
hdmi_audio_96k=0 ; set to 1 for 96khz/16bit HDMI audio (48khz/16bit otherwise)
keyrah_mode=0x18d80002 ; VIDPID of keyrah for special code translation (0x23418037 for Arduino Micro)
vscale_mode=0 ; 0 - scale to fit the screen height.
; 1 - use integer scale only.
; 2 - use 0.5 steps of scale.
; 3 - use 0.25 steps of scale.
vscale_border=0 ; set vertical border for TVs cutting the upper/bottom parts of screen (1-399)
;bootscreen=0 ; uncomment to disable boot screen of some cores like Minimig.
;mouse_throttle=10 ; 1-100 mouse speed divider. Useful for very sensitive mice
rbf_hide_datecode=0 ; 1 - hides datecodes from rbf file names. Press F2 for quick temporary toggle
menu_pal=0 ; 1 - PAL mode for menu core
hdmi_limited=0 ; 1 - use limited (16..235) color range over HDMI
; 2 - use limited (16..255) color range over HDMI, for VGA converters.
direct_video=0 ; 1 - enable core video timing over HDMI, use only with VGA converters.
fb_size=0 ; 0 - automatic, 1 - full size, 2 - 1/2 of resolution, 4 - 1/4 of resolution.
fb_terminal=1 ; 1 - enabled (default), 0 - disabled
osd_timeout=30 ; 5-3600 timeout (in seconds) for OSD to disappear in Menu core. 30 seconds if not set.
; Background picture will get darker after double timeout
osd_rotate=0 ; Display OSD menu rotated, 0 - no rotation, 1 - rotate right (+90°), 2 - rotate left (-90°)
Hope this helps