Hi

You can prepare single config file by inputting paired end reads ( used for obtaining the contigs), mate-pairs of 3k and 8k and SOAPDenovo2. You should mention the following flags in config file to decide when (rank) and for what ((asm_flags) the reads should be used .

In your case you should use as follows

For paired end reads:

asm_flags=1 & rank=1

For 3k MP:

asm_flags=2 & rank=2

For 8k MP:

asm_flags=2 & rank=3

You can follow the below link regarding insert size calculation.

Estimate Insert Size In Paired-End/Mate-Pair

I hope this helps!