Q1 Every time you change the timeframe the EA resets so it is similar to attach it again to the chart. Changing the timeframe is not recommended unless you really know what you are doing. For example in one time frame the logic will look at the indicator values and will say Buy, if you go to another timeframe the indicator values may say SELL.
When the EA starts it checks for existing positions. If there are existing positions it shows that warning for you to be aware and take action. It is just that "a warning".
For example, after changing the timeframe you see the warning, you may say my ea should buy but it does not so you will complain and say the ea does not work. Probably if there are existing positions the ea will not buy because the max number of positions has been reached. The warning is there for you to think how is this going to affect my ea.
For Q2, read the set up guide at
http://www.molanis.com/images/stories/m ... olanis.pdfYou need to set up the mt4 directory which seems to be pointing to the wrong directory. it should be like C:\Program Files\MetaTrader 4
The other part to set up is the mql4 directory. That seems to be fine or you would not see the ea in mt4