Hi, 

I have few quick question regarding macs14?

-  How one can treat the replicates? Do I have to run separately and then take average from the final peaks or is there any way to include it in one run?

-   macs14 generates two wig files under "--single-profile" option; one for control and one for treated. which file to use for plotting final peak profile? Do I have to subtract treated - control manually or does it give the final peak wig files?

Thanks in advance
If you have the replicate, you can take the consistent peaks called in both replicates. There will be variability in ChIP-Seq data, so sometimes you may want to consider union of peaks instead of intersections.

Regarding peak profile, by control do you mean input ? or control in the sense of WT/KO ? You can plot both the treated and control using deeptools2 so that it will be clear that both separated if that's the intention. For UCSC tracks, I would get the bigwigs with -log10(p-value), to show enrichment over inputs. 