PCBgogo

Hello, I've started working in PCB design and assembly.
I do the layout and the component assembly. The PCB itself while in prototyping phase is manufactured "in-house" by other technicians. They use substractive method with a CNC milling machine. There are good things and bad things on doing it in-house. We get to do relatively fast and cheap prototyping. 
Drawbacks: 

· Unreliable vias (I use thin wire or resistor leads if the trace has to carry power)

· No solder mask

· The tolerance on the milling tool makes it so that we can't have really thin traces, and pads get thinner than designed

Any recommendations to mitigate the problems that this drawbacks create? I think that when I bridged to legs of the smallest component when reflowing was do to the lack of solder mask and the pads being too thin and taking too little solder on them so it went upwards on the legs.
We'll need to do at least 20 PCBs and hopefully when we finish prototyping and get the design right we'll send it to manufacture outside, so it'll be proper professional PCB.
The PCB is SMT and double sided. Passives down to 0603(imperial) and the smallest IC has a 0.6mm pin pitch (TPS6212x). I can solder all of them by hand using soldering iron, but I hoped to get better results and for the assembly to be faster with reflow, be it using a hot air station or a reflow oven (we've one). 
I looked into it and in some places i found that you can actually reflow the board two times (one for each side) and if the components are not too heavy they won't fall when you reflow the other side. Does that actually work or is it unreliable? And is it the best way to solder them or is there a better way for what I've to do? I guess when we have them made professionally we could even get the stencils for faster solder paste application.
While I was soldering and testing parts of the prototype one prototype board, apart from the legs getting a solder bridge (as i explained earlier) I also found another problem while reflowing (with the hot air station). Some pads were already properly reflowed and had a nice solder joint but others even after a much longer time under the hot air didn't reflow properly. The solder was "soft" i could deform it with the tweezers. 
Could it be due to the solder paste being expired (1 year expired or so), or would it be more likely due to me doing something bad? Maybe they had bigger thermal mass? But I really stayed quite longer on those after some already reflowed... I think that all we use is lead free, if that makes any difference.
Where can I get proper information whether solder paste goes bad or not and how to identify it?
Thanks much in advance.