Married filing jointly,spouse just started doing independent contractor work (sole proprietor). Needs to file quarterly so how does that affect when filing annual return?

his self employment income and expenses are reported on schedule C.   assuming his net SE income is over $400, in additional to regular income taxes., you will owe SE employment tax which is about 14% of net SE income.     the IRS requires that taxes be paid in on a quarterly basis.  the is withholding is deemed paid evenly throughout the year unless you want to use the actual amount paid each quarter,  in addition quarterly estimated  tax payments (basically the total of taxes owed for the year that are in excess of withholding)  beed to be paid in 25% each quarter by 4/15 5/15 9/15 and /15/5/2020

in your case since he just started doing IC work, to reduce or avoid penalties you'll be able to complete form 2210 using the annualized installment method.

there are other ways to avoid underpayment of estimated tax penalties.  review form 2210

https://www.irs.gov/pub/irs-pdf/f2210.pdf

even if you do end up owing these penalties, you can request a waiver Part II box A. 

but must met the following

Waiver of Penalty
If you have an underpayment, all or part of the penalty for that
underpayment will be waived if the IRS determines that:
• In 2017 or 2018, you retired after reaching age 62 or became
disabled, and your underpayment was due to reasonable cause
(and not willful neglect), or
• The underpayment was due to a casualty, disaster, or other
unusual circumstance, and it would be inequitable to impose the
penalty. For federally declared disaster areas, see Federally
declared disaster.
To request any of the above waivers, do the following.
1. Check box A or box B in Part II.
a. If you checked box A, complete only page 1 of Form 2210
and attach it to your tax return (you aren't required to figure the
amount of penalty to be waived).
b. If you checked box B, complete Form 2210 through line 16
(or if you use the regular method, line 26 plus the penalty worksheet,
later) without regard to the waiver. Enter the amount you want
waived in parentheses on the dotted line next to line 17 (line 27 for
the regular method). Subtract this amount from the total penalty you
figured without regard to the waiver, and enter the result on line 17
(line 27 for the regular method).
2. Attach Form 2210 and a statement to your return explaining
the reasons you were unable to meet the estimated tax
requirements and the time period for which you are requesting a
waiver.
3. If you are requesting a waiver due to retirement or disability,
attach documentation that shows your retirement date (and your age
on that date) or the date you became disabled.
4. If you are requesting a waiver due to a casualty, disaster
(other than a federally declared disaster as discussed next), or other
unusual circumstance, attach documentation such as copies of
police and insurance company reports.
The IRS will review the information you provide and decide
whether to grant your request for a waiver.
Tax reform waiver. If you are an individual taxpayer and you
would otherwise owe an estimated tax penalty, the IRS will waive the
penalty under certain conditions. You would otherwise owe a penalty
if line 9 is more than line 6 after completing Part I of Form 2210, and
you have an amount of more than zero on line 27 after completing
Part IV (or on line 17 of Part III if you qualify to use the Short
Method). If you would otherwise owe a penalty, complete the 80%
Exception Worksheet below to see if you meet the conditions to be
eligible to claim the waiver. If so, you must check Box A in Part II,
write "80% Waiver" next to Box A, and file page 1 of Form 2210 with
your return to request the waiver. Do not file an additional statement
or attachment to claim the waiver.
Tax reform waiver refund. If you qualify for the tax refor