How do I make sure my electronics design is good from manufacturing perspective?
There's a thousand things to consider to reduce manufacturing costs, but some of the important ones are


Build in high volume. This spreads the set-up costs for a batch across more units. You'll find, for example, that the cost of board blanks drops extremely fast as you increase the batch size.
Negotiate your component costs. List price is just a starting point for negotiation. And once you've started buying in volume and your vendors know you're serious (and not going to need more support), go back and negotiate again. (To have a stronger position, design in multi-sourced components wherever possible)
Reduce process steps. For example, via-in-pad plated-over adds steps to board manufacturing, and mixing SMT with through-hole components adds steps to assembly. 
Reduce the number of lines in the BOM. This reduces effort for purchasing and increases the volume you're purchasing for each part number. For example, if you have both 49.9 and 51.1 ohm resistors, check if you can just make them all the same value. Or, if you have 3 linear regulators with different output voltages, use the same adjustable type for all of them instead of 3 different fixed-output parts. 
Design in as much tolerance as you can. For example, don't use 4 mil tracks if you can use 6 mil tracks. Don't specify +/- 10 mils on the board size if you can live with +/- 25 mils. Etc. The looser your tolerances, the better your yield. Even better, if you can make a tolerance loose enough, you might even eliminate the need to test it in final test.
Make your boards smaller. The more boards that fit on a standard panel, the lower the material cost.
Design in testability. This might mean adding test points for a bed-of-nails tester or it might mean making the design able to test all necessary features by itself (BIST).
Use standard processes rather than exotic ones: hot-air solder level instead of gold plating, through vias rather than blind vias, green solder mask rather than red, etc., etc.