there are certain "correct" ways to place what type of effects before after the other.
do a search on google.com on effect placements etc and read up some basics of it. Its not hard and fast but at least its the basics to get a good regular guitar sound.
Then envision your multieffects as single units.
for eg.
Single pedal = Boss Reverb RV3, Crybaby Wah GCB-95
Multieffects = Boss GT6
For some reason you don't like to use the built in reverb on the GT6. So where shall you put the reverb?
As the last pedal since you want to REVERB the whole guitar signal that have probably gone thro
[distortion, EQ, Chorus, delay] then Boss RV3
If you put it in first it will look like
Boss RV3, [distortion, EQ, Chorus, delay]
That will look VERY wrong in the eyes of most players but very right for some minority players.
Likewise. For the GCB95 wah.
GCB95 [distortion, EQ, Chorus, delay]
OR
[distortion, EQ, Chorus, delay] GCB95?
Do some reading on effects placement and you'll have a better idea. Also do note that you can't insert any pedals into the middle of the chain of MOST multieffects. There are some limitations to this. eg below.
[distortion, EQ, EH SMALL STONE CHORUS, delay]