Dual passports, choose when and where to use them carefully
I'm in the same boat, I have Dual nationality with Australia and Switzerland. I used both passports when travelling from Australia to Oslo, overland via SEAsia, India, Nepal, Pakistan, Iran, Turkey to Europe then Norway. I decided to use my Aussie passport in SEAsia but Swiss from Nepal/India onwards. For a few reasons.
1) Swiss army doesn't have troops in Pakistan and Afghanistan unlike Australia
2) Swiss visa price was cheaper for Turkey (free) and Nepal
3) Easier to travel in Europe as a Swiss than an Aussie (unfortunately we have a bad reputation and are cheap so a lot of places don't like us, just because of a few bad apples)
There are a few things you have to be careful of is when switching passports.
a) Obviously if you are stamped into a country on one passport you can't leave on another. Customs check this, and anyway you wouldn't get two visas, one in each passport it's just too expensive.
b) Customs & border control are not stupid, if you try to cross a border with a passport that doesn't have any stamps from your previous country then it will look suspect. The only time this works, is if the previous country doesn't put any stamps or any visas in your passport.
c) If you're travelling with multiple passports then you need to consider whether you inform embassy of just one or both countries of your travel itinerary in case of problems. (for AU see smartraveller.gov.au)
I/We never had an issue with borders checking the country of registration against the country of our passport. The important thing is that your registration papers are up to date and have your name, matching your passport(s).
Hope this helps.