Hi, my pedals are: Crybaby GCB-95, Boss MT-2 (i know...), Boss DS-1, Behringer Compressor Sustainer, Boss AC-2 and Boss NS-2. At the momment I am forced to put these into the front of my amp but I will soon be able to buy more cables to put some through the effects loop.
Could someone please tell me what order to have them in just going through the regular input and then what order to put them in once I have cables and are able to put some through the effects loop

For me I would go overdrive/distortion, wah, compressor in front of the amp and then any reverb/delay/chorus in the effects loop.

I have read some arguments about phasers with regards to putting them in front of the amp or in the loop. I put mine in front. Experimentation is a good thing for the sound combo you are after.
I would check the manuals for Boss Stompboxes. They generally show in front of the amp use because in many cases they cant handle the line levels coming from an effects loop. The specs should tell you what levels they can withstand then look at your amps specs and see what level it sends out and expects back.

Here's an article that explains the possible issues a little more...
Premier Guitar Effects loops
Moving on.....
Last edited by KenG at May 28, 2016,
Going from the guitar to the amp, go guitar -> Crybaby -> MT-2/DS-1 -> AC-2 -> NS-2.

If you use the FX loop, run the NS-2 using the X pattern (google it if unsure).

No idea where to put the Compressor Sustainer, never used one myself.

The order for the MT-2/DS-1 won't matter as I assume you are not using them both at once.
I would go wah, compressor then Od/distortion. After that you'll do your effects. My board is chorus - flanger - reverb. When I have my delay on my board it goes before reverb.
I also just switched from using my fx loop to going into the front of the amp as I find it makes the effects more out there.

The good thing though, is there isn't really a standard pedal order and you can place anything wherever you like.