You're only saving the latest count.

Try adding the new count to another var on each pass;
Code:
W1 var BYTE 
X1 var byte
X1=0
PORTC.4 = 0 ;leds off
PORTD.3 = 0

Main:

count PORTC.5, 1000, W1
X1=X1+W1 ' accumulate counts
lcdout $fe,1, dec W1
lcdout $fe,$c0, dec X1
pause 10
goto Main