You don't actually have to clarify your fee basis as a percent of construction cost, or $/SF, etc. The fee in your proposal should probably be a lump sum or time/material "hourly" rate structure (perhaps not to exceed) as suggested. You should run through a couple of these different iterations/approaches to arrive at a comfortable fee--compare the various methods suggested.
As an example of standard approach (assuming I'm not doing an industrial job and it leans itself to a more commercial type), I first figure the value of say the mechanical construction effort via Means or other similar resource (e.g., RSMeans Square Foot Costs). This book also has architect fee percentiles, but other better resources include PSMJ's "A/E Fees and Pricing Survey" and ZweigWhite's "Fee & Billing Survey of AEP&Env Firms". This will give you some good ideas on what other firms are doing and the percentiles will vary with the type of building, etc.
All three cited resources are annually issued products, and therefore there are costs associated with keeping up to date with these items.
I personnaly like to play with a spreadsheet with hourly billing rates assigned to the individuals/classes of personnel I will actually use on a job, and then plug in some hours based on various specific tasks (e.g, meetings, field trips, CAD time, etc.) and see if we can do it in that amount of time/for that amount of money.