Hi Nimesh - welcome to the community!
For eQuest, I personally advise building your proposed model first to match the actual design, then utilize Appendix G as a prescriptive reference to modify a copy of that proposed model to create your baseline. This approach avoids a slew of "what if" questions and potential re-working of your efforts encountered taking the opposite approach.
To your specific questions:
1. Appendix G directs you to select and define the correct baseline system type, determine capacity with a "sizing run" (using prescribed oversizing factors), then identify the correct efficiencies from the chapter 6 tables of 90.1 using the results of that sizing simulation. Before defining efficiencies, that happens to be the ideal time to review and resolve any excessive unmet hours, by the way.
2. Infiltration in the baseline should generally match that of the proposed. That's to say, don't touch those inputs when creating your baseline model. The only exception to this would be if you are trying to demonstrate some marked improvement in airtightness for an existing, retrofitted envelope, or if you are otherwise trying to document some exceptional infiltration-related credit. In either of those cases you should plan to include explanation & justification for why the infiltration inputs differ for model documentation.
There are a variety of resources/documents out there - what has worked best for me is to read and re-read Appendix G many times - the process is in there, it's just not written as clearly as it could be! I came into energy modeling with a general familiarity of all of 90.1, so that helped as well - if you haven't skimmed the preceding chapters and appendices I would recommend doing so at least once to know what's there: much of it is useful for reference when performing energy modeling. For further specific questions, you'll find these mailing lists and the associated archives pretty well cover everything that isn't very explicit in 90.1.
Best of luck!
~Nick
[cid:489575314 at 22072009-0ABB]
NICK CATON, P.E.