Make a list of "Needs" & "Wants": This list should have all the things
your home (and you) cannot live without, and needs to be included in the remodel. The 'Wants" list should be all the things your house and you would like included, but are more on the luxury end of the spectrum, rather than essential.
Your design professional and contractor will be able to assist you in narrowing these down to fit into your budget and design.

Create a Budget: Have in mind what you can spend. This may come from your savings account, a home equity line of credit, or other source. If you have specific materials, or products you wish to include, go and price them, or get bids on them. You may also consider phasing your project over a couple of years to get your needs and wants included; i.e., do the Master Bedroom Suite & Kitchen now...saving other portions for the next phase...and once you get more money. Please also remember, you will most likely spend up to 20% more than your initial bids; see #7, below.

Hire a Design Professional: Once you are armed with your 'Needs & Wants' & your Budget, hire an Architect or Architectural Designer. You will need to budget this in as well. Most banks have an allotment built in to a home equity line of credit, or construction loan, for such professional services. These services will range depending upon your needs. Fees for such services can be as little as $500 and as much as 15% of the cost to build the home. However, your money will be well spent. These professionals have the design prowess to assess your 'Needs & Wants', achieve them in a way architecturally pleasing to the
eye, and help you stay in budget. If you cannot afford to hire their full
services, hire them for a few sketches of design, or a few hours of consultation throughout the project. You will be pleased with the end result.

Certified Home Inspection: These professionals help to assess what's in and on your house that needs the most attention. Make sure the one you hire is board certified. They may also be able to assess your home's structure and make sure your home is structurally sound to handle an addition/remodel. This info will be useful to your design professional.

ReSale: Get advise from your design professional, as well as a Real Estate Agent as to what you could do to your home that would give you the most 'bang for your buck'. You want to know what can be added or remodeled that will, a) not overbuild the house for the neighborhood's scale or price range, and b) be the most cost effective return on your investment. Kitchens and Master Bathrooms (or Master Bedroom Suites) are #1 and #2 on the best return on investment.

Appraisal: This is a step you will most likely do when getting a Home
Equity Line of Credit. You will also want to use this appraisal as a means to helping you compare prices and square footages to neighboring houses comparable to yours. This will help you to not overbuild your home, in scale or in cost, to the ones around it.

Be willing to Compromise / Pick your Battles: You will have things that arise that will be unexpected and that will cost you more money, that are done incorrectly, that are not on the plans, & that may not be what you, or your design professional, had envisioned for the home. This is where you 'Pick your Battles'. Decide, as these situations arise, if it works in the final vision of the home, or just needs redoing because it is done wrong. Stick by your guns.  But you also need to compromise. For example, if you can live with the cheaper
dishwasher, and just get a credit at the end with your contractor...or if you can live with it and upgrade one of your 'wish list' items.

Deadlines: Do's and Don'ts: You should request of your contractor a
 'schedule' of events. This is a timeline of the weeks and months outlined with what will be going on in your project at any given time. You should always plan on adding time for change orders, (because you will always have at least one) and this may not get written on the schedule. Also remember the big ticket timeline items, such as, Plumbing Fixtures & Hardware, Door Hardware, Custom Doors &  Cabinetry, most Furnishings, Appliances, most Flooring, and anything you have to special order. If at all possible, avoid the Holidays as the end result of your project. You will most likely be disappointed.

Hiring a General Contractor: Once you have the drawings, you can get bids on your project. You should get bids from at least three (3) reputable general contractors. Ask your friends, neighbors, and colleagues for references for a good contractor. Always ask the contractor for references from former projects.  Go and see them whenever possible. Seeing their good work is always a 'good thing'. Ask the contractor to return the set of drawings to you with your bid. A good rule of thumb is to choose the bid which is about the middle of the road in cost. Remember, during your project your Contractor is your hired professional. He/She can be a friend after they have completed the job to your satisfaction.

Have Fun: Most of all, enjoy the journey. Taking a house that you like
and watching it evolve into something that you love is something of a wonder. Those six months (or whatever) will go by regardless of your attitude. The things you can change are the things to fret over, otherwise, forget it. Your attitude rubs off on everyone working on your project as well. Take lots of pictures and enjoy your 'trip'!